Molecular dynamic simulations with glue potentials
NASA Astrophysics Data System (ADS)
Pasrija, Ritu; Srivastava, Sunita
2011-12-01
Glue potential is being widely used by number of scientists worldwide in order to predict surface properties and also to reconstruct surfaces of various metals and semiconductors [1]. In this work, glue potential has been used to carry out molecular dynamic simulations for energies of Al, Mg, Pb and Au. Results of MD simulations with glue potential have been compared with that of two body interaction potential. It is found that Au has the maximum stable energy configuration.
Molecular potentials and relaxation dynamics
Karo, A.M.
1981-03-27
The use of empirical pseudopotentials, in evaluating interatomic potentials, provides an inexpensive and convenient method for obtaining highly accurate potential curves and permits the modeling of core-valence correlation, and the inclusion of relativistic effects when these are significant. As an example, recent calculations of the chi/sup 1/..sigma../sup +/ and a/sup 3/..sigma../sup +/ states of LiH, NaH, KH, RbH, and CsH and the chi/sup 2/..sigma../sup +/ states of their anions are discussed. Pseudopotentials, including core polarization terms, have been used to replace the core electrons, and this has been coupled with the development of compact, highly-optimized basis sets for the corresponding one- and two-electron atoms. Comparisons of the neutral potential curves with experiment and other ab initio calculations show good agreement (within 1000 cm/sup -1/ over most of the potential curves) with the difference curves being considerably more accurate.
Molecular dynamics simulations of solutions at constant chemical potential.
Perego, C; Salvalaglio, M; Parrinello, M
2015-04-14
Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which 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, which 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 Constant Chemical Potential Molecular Dynamics (C?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?MD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers. PMID:25877568
Sciortino, Francesco
Structure and dynamics in hexagonal ice: A molecular dynamics simulation with an ab rinifio polarizable and flexible potential Francesco Sciortino and Giorgina Corongiu CRS4, Centro di Ricerca, Sviluppo December 1992) We perform a molecular dynamics simulation of the hexagonal solid phase of water, using
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations
de Groot, Bert
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
Hammes-Schiffer, Sharon
Nonadiabatic transition state theory and multiple potential energy surface molecular dynamics the adiabatic approximation, i.e., the assumption that nuclear motion evolves on a single potential energy surface. Many chemical rate processes involve multiple potential energy surfaces, however, and a number
Constant-temperature molecular-dynamics algorithms for mixed hard-core/continuous potentials
Houndonougbo, Yao; Laird, Brian Bostian
2002-07-03
We present a set of second-order, time-reversible algorithms for the isothermal (NVT) molecular-dynamics (MD) simulation of systems with mixed hard-core/continuous potentials. The methods are generated by combining real-time Nosé thermostats...
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
Májek, Peter; Elber, Ron
2009-01-01
A coarse grained potential for protein simulations and fold ranking is presented. The potential is based on a two-point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and re-sampling are in the spirit of the generalized ensemble approach. No native structure information (e.g. secondary structure) is used in the calculation of the potential, or in the simulation of a particular protein. The potential is subject to two tests: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set), and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys, and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than twenty nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. PMID:19291741
Spezia, Riccardo; Jeanvoine, Yannick; Vuilleumier, Rodolphe
2014-08-01
In this work we have developed a polarizable potential to study Cm(III) forming complexes with carbonate anions in liquid water. The potential was developed by employing an extension of the procedure that we used to study the hydration of lanthanoids(III) and actinoids(III). Force field performances were benchmarked against DFT results obtained by both geometry optimization and Car-Parrinello molecular dynamics. With this polarizable potential, we run extended molecular dynamics simulations in liquid water from which we were able to identify structural and dynamical properties of such systems. In particular, water exchange dynamics were analyzed in detail. We obtained an average of three water molecules in the first shell of Cm(III) that show a relatively fast exchange dynamic (faster than for bare ions). Summarizing these results, we were able to draw an analogy to the results from the lanthanoid(III) series. In particular, it seems that Cm(III) behaves more like Nd(III) than Gd(III), as one would expect based on the recent hydration results and on f orbital occupancy. PMID:25086768
Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation
Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru; Weber, William J.
2007-08-01
Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.
NASA Astrophysics Data System (ADS)
Starrett, C. E.; Daligault, J.; Saumon, D.
2015-01-01
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.
Angular-dependent matrix potentials for fast molecular-dynamics simulations of transition metals.
Dudarev, S L
2006-04-26
The significance of the part played by the angular-dependent components of forces associated with d-d bonding between atoms in a transition metal has long remained a subject of debate. While almost all the large-scale molecular dynamics simulations of collision cascades and radiation damage in transition metals and alloys are currently performed using spherically symmetric many-body potentials, density functional calculations exhibit a highly anisotropic pattern of charge density deformation in and around the core of interstitial atom defects. This paper describes a fast second-order matrix recursion-based algorithm for including effects of angular anisotropy of d-d bonds in a large-scale molecular dynamics simulation. PMID:21690746
Kreck, Cara A; Mancera, Ricardo L
2014-02-20
Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials. PMID:24467489
Kobryn, Alexander E; Nikoli?, Dragan; Lyubimova, Olga; Gusarov, Sergey; Kovalenko, Andriy
2014-10-16
We present a method of DPD simulation based on a coarse-grained effective pair potential obtained from the DRISM-KH molecular theory of solvation. The theory is first used to calculate the radial distribution functions of all-atom solute monomers in all-atom solvent and then to invert them into an effective pair potential between coarse-grained beads such that their fluid without solvent accounts for molecular specificities and solvation effects in the all-atom system. Bonded interactions are sampled in relatively short MD of the all-atom system and modeled with best multi-Gaussian fit. Replacing the heuristically defined conservative force potential in DPD, the coarse-grained effective pair potential is free from the artificial restrictions on potential range and shape and on equal volume of solute and solvent blobs inherent in standard DPD. The procedure is flexible in specifying coarse-grained mapping and enormously increases computational efficiency by eliminating solvent. The method is validated on polystyrene chains of various length in toluene at finite concentrations for room and polystyrene glass transition temperature. It yields the chain elastic properties and diffusion coefficient in good agreement with experiment and all-atom MD simulations. DPD with coarse-grained effective pair potential is capable of predicting both structural and dynamic properties of polymer solutions and soft matter with high accuracy and computational efficiency. PMID:25162701
Christian Bayer; Hakon Hoel; Ashraful Kadir; Petr Plechac; Mattias Sandberg; Anders Szepessy
2015-05-12
The difference of the values of observables for the time-independent Schroedinger equation, with matrix valued potentials, and the values of observables for ab initio Born-Oppenheimer molecular dynamics, of the ground state, depends on the probability to be in excited states and the electron/nuclei mass ratio. The paper first proves an error estimate (depending on the electron/nuclei mass ratio and the probability to be in excited states) for this difference of microcanonical observables, assuming that molecular dynamics space-time averages converge, with a rate related to the maximal Lyapunov exponent. The error estimate is uniform in the number of particles and the analysis does not assume a uniform lower bound on the spectral gap of the electron operator and consequently the probability to be in excited states can be large. A numerical method to determine the probability to be in excited states is then presented, based on Ehrenfest molecular dynamics and stability analysis of a perturbed eigenvalue problem.
Seniya, Chandrabhan; Khan, Ghulam Jilani; Uchadia, Kuldeep
2014-01-01
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
NASA Astrophysics Data System (ADS)
Tejada, I. G.; Brochard, L.; Stoltz, G.; Legoll, F.; Lelièvre, T.; Cancès, E.
2015-01-01
Molecular dynamics is a simulation technique that can be used to study failure in solids, provided the inter-atomic potential energy is able to account for the complex mechanisms at failure. Reactive potentials fitted on ab initio results or on experimental values have the ability to adapt to any complex atomic arrangement and, therefore, are suited to simulate failure. But the complexity of these potentials, together with the size of the systems considered, make simulations computationally expensive. In order to improve the efficiency of numerical simulations, simpler harmonic potentials can be used instead of complex reactive potentials in the regions where the system is close to its ground state and a harmonic approximation reasonably fits the actual reactive potential. However the validity and precision of such an approach has not been investigated in detail yet. We present here a methodology for constructing a reduced potential and combining it with the reactive one. We also report some important features of crack propagation that may be affected by the coupling of reactive and reduced potentials. As an illustrative case, we model a crystalline two-dimensional material (graphene) with a reactive empirical bond-order potential (REBO) or with harmonic potentials made of bond and angle springs that are designed to reproduce the second order approximation of REBO in the ground state. We analyze the consistency of this approximation by comparing the mechanical behavior and the phonon spectra of systems modeled with these potentials. These tests reveal when the anharmonicity effects appear. As anharmonic effects originate from strain, stress or temperature, the latter quantities are the basis for establishing coupling criteria for on the fly substitution in large simulations.
NASA Astrophysics Data System (ADS)
Zhang, Yongfeng; Millett, Paul C.; Tonks, Michael R.; Bai, Xian-Ming; Biner, S. Bulent
2014-09-01
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 <1 0 0> symmetrical tilt ?5 and the <1 1 0> symmetrical tilt ?3 ({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 ?3 boundary was found to be more prone to fracture than the ?5 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
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.
NASA Astrophysics Data System (ADS)
Yamashita, Takefumi
Accurate modeling of potential functions is critical for realistic molecular dynamics (MD) simulations. In this study, improvement in potential functions is discussed by revisiting the multistate empirical valence bond (MS-EVB) method and the FUJI force field. The MS-EVB method enables simulation of dynamic chemical reactions in various situations. In this study, excess protons in water under shear were investigated by combining the MS-EVB method with the non-equilibrium MD technique. It was found that the orientation of the hydronium-like moiety is considerably more anisotropic under shear than that of the water molecule. Separately, the FUJI force field includes main-chain torsional parameters carefully derived on the basis of high-level ab initio calculations. To further demonstrate that the use of the FUJI force field improves the accuracy of MD results beyond previously reported examples, the conformational distribution of the Ala dipeptide was investigated. The results obtained using the FUJI force field agreed more closely with the experimental results than those obtained using other standard force fields. Interestingly, the MD trajectories with the FUJI force field undergo the Y conformation more frequently than those with other popular force fields. Furthermore, it was found that the choice of force field affects the structures of an antigen-antibody complex obtained using MD simulations. These improvements in the force fields essentially extend the range of applications for the MD simulation method.
Kong, Ren; Chang, Shan; Xia, Weiming; Wong, Stephen T C
2015-08-01
Presenilin 1 (PS1) is the catalytic unit of ?-secretase which cleaves more than one hundred substrates. Among them, amyloid precursor protein (APP) and Notch are notable for their pivotal role in the pathogenesis of Alzheimer's disease (AD) and certain types of cancer. The hydrolysis process occurring inside the hydrophobic lipid bilayer remains unclear. With the aim to understand the mechanism of intramembrane proteolysis by ?-secretase, we constructed a homology model of human PS1 and performed molecular dynamics simulation in explicit membrane phospholipids with different components. During the simulation, TM9 was found to exhibit a high level of flexibility that involved in "gate-open" movement of TM2 and TM6, and thus partially exposed the catalytic residues. The highly conserved PALP motif acts as an anchor to mediate the conformation changes of TM6 induced by TM9. Moreover, direct interactions were observed between 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and the active site of ?-secretase, indicating that the lipid molecules have the potential to modulate ?-secretase by contacting with the catalytic residues, i.e., ASP 257 and ASP 385 of PS1. The intermediate states indicate a potential substrate penetration pathway through the interface of TM2 and TM6, which may be induced by changes of TM9. To our knowledge, this is the first molecular simulation study that reveals dynamic behavior of the human PS1 structure in the lipid bilayer and provides insight into the substrate entry path for subsequent intramembrane hydrolysis, which is critical information required for new strategy development of ?-secretase modulators to alleviate devastating AD. PMID:26142917
Redox potentials and acidity constants from density functional theory based molecular dynamics.
Cheng, Jun; Liu, Xiandong; VandeVondele, Joost; Sulpizi, Marialore; Sprik, Michiel
2014-12-16
CONSPECTUS: All-atom methods treat solute and solvent at the same level of electronic structure theory and statistical mechanics. All-atom computation of acidity constants (pKa) and redox potentials is still a challenge. In this Account, we review such a method combining density functional theory based molecular dynamics (DFTMD) and free energy perturbation (FEP) methods. The key computational tool is a FEP based method for reversible insertion of a proton or electron in a periodic DFTMD model system. The free energy of insertion (work function) is computed by thermodynamic integration of vertical energy gaps obtained from total energy differences. The problem of the loss of a physical reference for ionization energies under periodic boundary conditions is solved by comparing with the proton work function computed for the same supercell. The scheme acts as a computational hydrogen electrode, and the DFTMD redox energies can be directly compared with experimental redox potentials. Consistent with the closed shell nature of acid dissociation, pKa estimates computed using the proton insertion/removal scheme are found to be significantly more accurate than the redox potential calculations. This enables us to separate the DFT error from other sources of uncertainty such as finite system size and sampling errors. Drawing an analogy with charged defects in solids, we trace the error in redox potentials back to underestimation of the energy gap of the extended states of the solvent. Accordingly the improvement in the redox potential as calculated by hybrid functionals is explained as a consequence of the opening up of the bandgap by the Hartree-Fock exchange component in hybrids. Test calculations for a number of small inorganic and organic molecules show that the hybrid functional implementation of our method can reproduce acidity constants with an uncertainty of 1-2 pKa units (0.1 eV). The error for redox potentials is in the order of 0.2 V. PMID:25365148
First principles molecular dynamics of metal/water interfaces under bias potential
NASA Astrophysics Data System (ADS)
Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi
2014-03-01
Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.
Redox potentials and pKa for benzoquinone from density functional theory based molecular dynamics.
Cheng, Jun; Sulpizi, Marialore; Sprik, Michiel
2009-10-21
The density functional theory based molecular dynamics (DFTMD) method for the computation of redox free energies presented in previous publications and the more recent modification for computation of acidity constants are reviewed. The method uses a half reaction scheme based on reversible insertion/removal of electrons and protons. The proton insertion is assisted by restraining potentials acting as chaperones. The procedure for relating the calculated deprotonation free energies to Brønsted acidities (pK(a)) and the oxidation free energies to electrode potentials with respect to the normal hydrogen electrode is discussed in some detail. The method is validated in an application to the reduction of aqueous 1,4-benzoquinone. The conversion of hydroquinone to quinone can take place via a number of alternative pathways consisting of combinations of acid dissociations, oxidations, or dehydrogenations. The free energy changes of all elementary steps (ten in total) are computed. The accuracy of the calculations is assessed by comparing the energies of different pathways for the same reaction (Hess's law) and by comparison to experiment. This two-sided test enables us to separate the errors related with the restrictions on length and time scales accessible to DFTMD from the errors introduced by the DFT approximation. It is found that the DFT approximation is the main source of error for oxidation free energies. PMID:20568869
Hua Y. Geng
2014-12-19
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 $r_{s}=0.912$.
Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van
2014-07-01
Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.
Implementing Molecular Dynamics on Hybrid High Performance Computers - Three-Body Potentials
Brown, W Michael; Yamada, Masako
2013-01-01
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 re- quirements. 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 efficiently use accelerators to improve the performance of molecular dynamics (MD) 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 algo- rithms 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.
Implementing molecular dynamics on hybrid high performance computers—Three-body potentials
NASA Astrophysics Data System (ADS)
Brown, W. Michael; Yamada, Masako
2013-12-01
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.
Sattelle, Benedict M; Sutcliffe, Michael J
2008-12-18
The tricyclic isoalloxazine nucleus of the redox cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) acts as an electron sink in life-sustaining biological electron transfer (eT). The functional diversity of flavin-containing proteins (flavoproteins) transcends that of free flavins. A large body of experimental evidence attributes natural control of flavoprotein-mediated eT to tuning of the thermodynamic driving force by the protein environment. Understanding and engineering such modulation by the protein environment of the flavin redox potential (DeltaE(o)) is valuable in biotechnology and device design. In this study we employed classical molecular dynamics free energy simulations (MDFES), within a thermodynamic integration (TI) formalism, to calculate the change in FMN first reduction potential (DeltaDeltaE(o)(ox/sq)) imparted by 6 flavoprotein active site mutations. The combined performance of the AMBER ff03 (protein) and GAFF (cofactor) force fields was benchmarked against experimental data for mutations close to the isoalloxazine re- and si-faces that perturb the wild-type DeltaE(o)(ox/sq) value in Anabaena flavodoxin. The classical alchemical approach used in this study overestimates the magnitude of DeltaE(o) values, in common with other studies. Nevertheless, chemically accurate DeltaDeltaE(o) values--calculated to within 1 kcal mol(-1) of the experimental value--were obtained for five of the six mutations studied. We have shown that this approach is practical for quantitative in silico screening of the effect of mutations on the first reduction potential where experimental values and structural data are available for the wild-type flavoprotein. This approach promises to be useful as an integral part of future interdisciplinary strategies to engineer desired thermodynamic properties in flavoproteins of biotechnological interest. PMID:18828581
NASA Astrophysics Data System (ADS)
Wu, Xiaojie; Li, Xiantao
2015-01-01
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.
Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential.
Zhou, Xiaowang; Ward, Donald K; Wong, Bryan M; Doty, F Patrick; Zimmerman, Jonathan A
2012-08-23
Cd(1-x)Zn(x)Te (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals. PMID:22962626
Refining Homology Models by Combining Replica-Exchange Molecular Dynamics and Statistical Potentials
Zhu, Jiang; Fan, Hao; Periole, Xavier; Honig, Barry; Mark, Alan E.
2009-01-01
A protocol is presented for the global refinement of homology models of proteins. It combines the advantages of temperature-based replica-exchange molecular dynamics (REMD) for conformational sampling and the use of statistical potentials for model selection. The protocol was tested using 21 models. Of these 14 were models of 10 small proteins for which high-resolution crystal structures were available, the remainder were targets of the recent CASPR exercise. It was found that REMD in combination with currently available force fields could sample near-native conformational states starting from high-quality homology models. Conformations in which the backbone RMSD of secondary structure elements (SSE-RMSD) was lower than the starting value by 0.5 to 1.0 Å were found for 15 out of the 21 cases (average 0.82 Å). Furthermore, when a simple scoring function consisting of two statistical potentials was used to rank the structures, one or more structures with SSE-RMSD of at least 0.2 Å lower than the starting value was found among the 5 best ranked structures in 11 out of the 21 cases. The average improvement in SSE-RMSD for the best models was 0.42 Å. However, none of the scoring functions tested identified the structures with the lowest SSE-RMSD as the best models although all identified the native conformation as the one with lowest energy. This suggests that while the proposed protocol proved effective for the refinement of high-quality models of small proteins scoring functions remain one of the major limiting factors in structure refinement. This and other aspects by which the methodology could be further improved are discussed. PMID:18338384
Introduction to Accelerated Molecular Dynamics
Perez, Danny [Los Alamos National Laboratory
2012-07-10
Molecular Dynamics is the numerical solution of the equations of motion of a set of atoms, given an interatomic potential V and some boundary and initial conditions. Molecular Dynamics is the largest scale model that gives unbiased dynamics [x(t),p(t)] in full atomistic detail. Molecular Dynamics: is simple; is 'exact' for classical dynamics (with respect to a given V); can be used to compute any (atomistic) thermodynamical or dynamical properties; naturally handles complexity -- the system does the right thing at the right time. The physics derives only from the interatomic potential.
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
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.
Massobrio, C.; Pontikis, V.; Martin, G.
1989-03-06
We present the first molecular-dynamics study of the amorphization of a crystalline alloy (NiZr/sub 2/) induced by chemical disorder. We used a n-body potential in conjunction with isobaric-isothermal molecular dynamics. The behavior of the pair distribution function suggests that the instability leading to the amorphous state is a first-order phase transformation.
Molecular-dynamics study of 2-D melting: long-range potentials
Kalia, R.K.; Vashishta, P.
1981-01-01
Melting of a two-dimensional electron lattice and a two-dimensional dipolar solid are studied using molecular-dynamics techniques. The existence of hysteresis and latent heat of melting are observed, and the melting transitions in the two cases are found to be first order. For an electron lattice the melting occurs between GAMMA=129 +- 3 whereas in the dipolar solid it is between GAMMA=62 +- 3, with a transition entropy of 0.3 k/sub B/ per particle for both the systems.
NASA Astrophysics Data System (ADS)
Methfessel, M.; van Schilfgaarde, M.
A major advance in electronic structure calculations was the combination of local-density techniques with molecular dynamics by Car and Parrinello seven years ago. Unfortunately, application of the Car-Parrinello scheme has been limited essentially to sp materials because only in the plane-wave pseudopotential method forces are trivial to calculate. We present a systematic approach to derive force theorems with desired characteristics within complicated basis sets, which are applicable to all elements of the periodic table equally well. Application to the LMTO basis set yields an accurate force theorem, quite distinct from the Hellman-Feynman form, which is exceptionally insensitive to errors in the trial density. The forces were implemented in a new full-potential LMTO method which is suited to arbitrary geometries. First results for ab-initio molecular dynamics and simulated annealing runs are shown for some random small molecules and small clusters of silver atoms.
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter
2015-01-01
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance. PMID:26103621
Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Mollica, Luca; Decherchi, Sergio; Zia, Syeda Rehana; Gaspari, Roberto; Cavalli, Andrea; Rocchia, Walter
2015-06-01
Drug discovery is expensive and high-risk. Its main reasons of failure are lack of efficacy and toxicity of a drug candidate. Binding affinity for the biological target has been usually considered one of the most relevant figures of merit to judge a drug candidate along with bioavailability, selectivity and metabolic properties, which could depend on off-target interactions. Nevertheless, affinity does not always satisfactorily correlate with in vivo drug efficacy. It is indeed becoming increasingly evident that the time a drug spends in contact with its target (aka residence time) can be a more reliable figure of merit. Experimental kinetic measurements are operatively limited by the cost and the time needed to synthesize compounds to be tested, to express and purify the target, and to setup the assays. We present here a simple and efficient molecular-dynamics-based computational approach to prioritize compounds according to their residence time. We devised a multiple-replica scaled molecular dynamics protocol with suitably defined harmonic restraints to accelerate the unbinding events while preserving the native fold. Ligands are ranked according to the mean observed scaled unbinding time. The approach, trivially parallel and easily implementable, was validated against experimental information available on biological systems of pharmacological relevance.
Jacobson, Daniel; Stratt, Richard M
2014-05-01
Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation-molecules largely thread their way through narrow channels available in the potential energy landscape. PMID:24811642
NASA Astrophysics Data System (ADS)
Jacobson, Daniel; Stratt, Richard M.
2014-05-01
Because the geodesic pathways that a liquid follows through its potential energy landscape govern its slow, diffusive motion, we suggest that these pathways are logical candidates for the title of a liquid's "inherent dynamics." Like their namesake "inherent structures," these objects are simply features of the system's potential energy surface and thus provide views of the system's structural evolution unobstructed by thermal kinetic energy. This paper shows how these geodesic pathways can be computed for a liquid of linear molecules, allowing us to see precisely how such molecular liquids mix rotational and translational degrees of freedom into their dynamics. The ratio of translational to rotational components of the geodesic path lengths, for example, is significantly larger than would be expected on equipartition grounds, with a value that scales with the molecular aspect ratio. These and other features of the geodesics are consistent with a picture in which molecular reorientation adiabatically follows translation—molecules largely thread their way through narrow channels available in the potential energy landscape.
Kumar, R. Barani; Suresh, M. Xavier; Priya, B. Shanmuga
2015-01-01
Background: The alpha-delta bungartoxin-4 (?-?-Bgt-4) is a potent neurotoxin produced by highly venomous snake species, Bungarus caeruleus, mainly targeting neuronal acetylcholine receptors (nAchRs) and producing adverse biological malfunctions leading to respiratory paralysis and mortality. Objective: In this study, we predicted the three-dimensional structure of ?-?-Bgt-4 using homology modeling and investigated the conformational changes and the key residues responsible for nAchRs inhibiting activity. Materials and Methods: From the selected plants, which are traditionally used for snake bites, the active compounds are taken and performed molecular interaction studies and also used for modern techniques like pharmacophore modeling and mapping and absorption, distribution, metabolism, elimination and toxicity analysis which may increase the possibility of success. Results: Moreover, 100's of drug-like compounds were retrieved and analyzed through computational virtual screening and allowed for pharmacokinetic profiling, molecular docking and dynamics simulation. Conclusion: Finally the top five drug-like compounds having competing level of inhibition toward ?-?-Bgt-4 toxin were suggested based on their interaction with ?-?-Bgt-4 toxin. PMID:26109766
NASA Astrophysics Data System (ADS)
Lin, Xubo; Bai, Tingting; Zuo, Yi Y.; Gu, Ning
2014-02-01
Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery.Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr04163h
Rich, Sarah Celeste
2008-01-01
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 ...
Grenier, Romain; To, Quy-Dong; Lara-Castells, María Pilar de; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
Zhou, An; Hu, Jianping; Wang, Lirong; Zhong, Guochen; Pan, Jian; Wu, Zeyu; Hui, Ailing
2015-10-01
Acetylcholinesterase (AChE) is one of the key targets of drugs for treating Alzheimer's disease (AD). Tacrine is an approved drug with AChE-inhibitory activity. In this paper, 3D-QSAR, molecular docking, and molecular dynamics were carried out in order to study 60 tacrine derivatives and their AChE-inhibitory activities. 3D-QSAR modeling resulted in an optimal CoMFA model with q (2)?=?0.552 and r (2)?=?0.983 and an optimal CoMSIA model with q (2)?=?0.581 and r (2)?=?0.989. These QSAR models also showed that the steric and H-bond fields of these compounds are important influences on their activities. The interactions between these inhibitors and AChE were further explored through molecular docking and molecular dynamics simulation. A few key residues (Tyr70, Trp84, Tyr121, Trp279, and Phe330) at the binding site of AChE were identified. The results of this study improve our understanding of the mechanisms of AChE inhibitors and afford valuable information that should aid the design of novel potential AChE inhibitors. Graphical Abstract Superposition of backbone atoms of the lowest-energy structure obtained from MD simulation (magenta) onto those of the structure of the initial molecular docking model (green). PMID:26438408
NASA Astrophysics Data System (ADS)
Xu, Wen; Zhu, Liyan; Cai, Yongqing; Zhang, Gang; Li, Baowen
2015-06-01
A Stillinger-Weber interatomic potential is parameterized for phosphorene. It well reproduces the crystal structure, cohesive energy, and phonon dispersion predicted by first-principles calculations. The thermal conductivity of phosphorene is explored by equilibrium molecular dynamics simulations adopting the optimal set of potential parameters. At room temperature, the intrinsic thermal conductivities along zigzag and armchair directions are about 152.7 and 33.0 W/mK, respectively, with a large anisotropy ratio of five. The remarkably directional dependence of thermal conductivity in phosphorene, consistent with previous reports, is mainly due to the strong anisotropy of phonon group velocities, and weak anisotropy of phonon lifetimes as revealed by lattice dynamics calculations. Moreover, the effective phonon mean free paths at zigzag and armchair directions are about 141.4 and 43.4 nm, respectively.
Lin, Xubo; Bai, Tingting; Zuo, Yi Y; Gu, Ning
2014-03-01
Nanoparticles (NPs) show great promises in biomedical applications as the respiratory drug carrier system. Once reaching the alveolar region, NPs first interact with the pulmonary surfactant (PS) film, which serves as the first biological barrier and plays an important role in maintaining the normal respiratory mechanics. Therefore, understanding the interactions between NPs and PS can help promote the NP-based respiratory drug carrier systems. Using coarse-grained molecular dynamics simulations, we studied the effect of rigid spherical NPs with different hydrophobicity and sizes on a dipalmitoylphosphatidylcholine (DPPC) monolayer at the air-water interface. Four different NPs were considered, including hydrophilic and hydrophobic NPs, each with two diameters of 3 nm and 5 nm (the sizes are comparable to that of generation 3 and 5 PAMAM dendrimers, which have been widely used for nanoscale drug carrier systems). Our simulations showed that hydrophilic NPs can readily penetrate into the aqueous phase with little or no disturbance on the DPPC monolayer. However, hydrophobic NPs tend to induce large structural disruptions, thus inhibiting the normal phase transition of the DPPC monolayer upon film compression. Our simulations also showed that this inhibitory effect of hydrophobic NPs can be mitigated through PEGylation. Our results provide useful guidelines for molecular design of NPs as carrier systems for pulmonary drug delivery. PMID:24464138
Jover, J; Haslam, A J; Galindo, A; Jackson, G; Müller, E A
2012-10-14
We present a continuous pseudo-hard-sphere potential based on a cut-and-shifted Mie (generalized Lennard-Jones) potential with exponents (50, 49). Using this potential one can mimic the volumetric, structural, and dynamic properties of the discontinuous hard-sphere potential over the whole fluid range. The continuous pseudo potential has the advantage that it may be incorporated directly into off-the-shelf molecular-dynamics code, allowing the user to capitalise on existing hardware and software advances. Simulation results for the compressibility factor of the fluid and solid phases of our pseudo hard spheres are presented and compared both to the Carnahan-Starling equation of state of the fluid and published data, the differences being indistinguishable within simulation uncertainty. The specific form of the potential is employed to simulate flexible chains formed from these pseudo hard spheres at contact (pearl-necklace model) for m(c) = 4, 5, 7, 8, 16, 20, 100, 201, and 500 monomer segments. The compressibility factor of the chains per unit of monomer, m(c), approaches a limiting value at reasonably small values, m(c) < 50, as predicted by Wertheim's first order thermodynamic perturbation theory. Simulation results are also presented for highly asymmetric mixtures of pseudo hard spheres, with diameter ratios of 3:1, 5:1, 20:1 over the whole composition range. PMID:23061853
NASA Astrophysics Data System (ADS)
Ma, Qian; Dai, Jiayu; Kang, Dongdong; Zhao, Zengxiu; Yuan, Jianmin; Zhao, Xueqing
2014-12-01
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.
Open boundary molecular dynamics
NASA Astrophysics Data System (ADS)
Delgado-Buscalioni, R.; Sabli?, J.; Praprotnik, M.
2015-06-01
This contribution analyzes several strategies and combination of methodologies to perform molecular dynamic simulations in open systems. Here, the term open indicates that the total system has boundaries where transfer of mass, momentum and energy can take place. This formalism, which we call Open Boundary Molecular Dynamics (OBMD), can act as interface of different schemes, such as Adaptive Resolution Scheme (AdResS) and Hybrid continuum-particle dynamics to link atomistic, coarse-grained (CG) and continuum (Eulerian) fluid dynamics in the general framework of fluctuating Navier-Stokes equations. The core domain of the simulation box is solved using all-atom descriptions. The CG layer introduced using AdResS is located at the outer part of the open box to make feasible the insertion of large molecules into the system. Communications between the molecular system and the outer world are carried out in the outer layers, called buffers. These coupling preserve momentum and mass conservation laws and can thus be linked with Eulerian hydro- dynamic solvers. In its simpler form, OBMD allows, however, to impose a local pressure tensor and a heat flux across the system's boundaries. For a one component molecular system, the external normal pressure and temperature determine the external chemical potential and thus the independent parameters of a grand-canonical ensemble simulation. Extended ensembles under non-equilibrium stationary states can also be simulated as well as time dependent forcings (e.g. oscillatory rheology). To illustrate the robustness of the combined OBMD-AdResS method, we present simulations of star-polymer melts at equilibrium and in sheared flow.
Accelerated molecular dynamics methods
Perez, Danny [Los Alamos National Laboratory
2011-01-04
The molecular dynamics method, although extremely powerful for materials simulations, is limited to times scales of roughly one microsecond or less. On longer time scales, dynamical evolution typically consists of infrequent events, which are usually activated processes. This course is focused on understanding infrequent-event dynamics, on methods for characterizing infrequent-event mechanisms and rate constants, and on methods for simulating long time scales in infrequent-event systems, emphasizing the recently developed accelerated molecular dynamics methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics). Some familiarity with basic statistical mechanics and molecular dynamics methods will be assumed.
NASA Astrophysics Data System (ADS)
Allen, Roland; Jiang, Chen-Wei; Zhang, Xiu-Xing; Fang, Ai-Ping; Li, Hong-Rong; Xie, Rui-Hua; Li, Fu-Li
2015-03-01
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. Research Fund for the Doctoral Program of Higher Education of China; Fundamental Research Funds for the Central Universities; Robert A. Welch Foundation; National Natural Science Foundation of China.
Fan, Zheyong; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari
2015-01-01
We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems descried by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimen...
NASA Astrophysics Data System (ADS)
Fan, Zheyong; Pereira, Luiz Felipe C.; Wang, Hui-Qiong; Zheng, Jin-Cheng; Donadio, Davide; Harju, Ari
2015-09-01
We derive expressions of interatomic force and heat current for many-body potentials such as the Tersoff, the Brenner, and the Stillinger-Weber potential used extensively in molecular dynamics simulations of covalently bonded materials. Although these potentials have a many-body nature, a pairwise force expression that follows Newton's third law can be found without referring to any partition of the potential. Based on this force formula, a stress applicable for periodic systems can be unambiguously defined. The force formula can then be used to derive the heat current formulas using a natural potential partitioning. Our heat current formulation is found to be equivalent to most of the seemingly different heat current formulas used in the literature, but to deviate from the stress-based formula derived from two-body potential. We validate our formulation numerically on various systems described by the Tersoff potential, namely three-dimensional silicon and diamond, two-dimensional graphene, and quasi-one-dimensional carbon nanotube. The effects of cell size and production time used in the simulation are examined.
Molecular dynamics simulations.
Lindahl, Erik R
2008-01-01
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that, respectively, optimize structure and simulate the natural motion of biological macromolecules. The common theoretical framework based on statistical mechanics is covered briefly as well as limitations of the computational approach, for instance, the lack of quantum effects and limited timescales accessible. As a practical example, a full simulation of the protein lysozyme in water is described step by step, including examples of necessary hardware and software, how to obtain suitable starting molecular structures, immersing it in a solvent, choosing good simulation parameters, and energy minimization. The chapter also describes how to analyze the simulation in terms of potential energies, structural fluctuations, coordinate stability, geometrical features, and, finally, how to create beautiful ray-traced movies that can be used in presentations. PMID:18446279
NASA Astrophysics Data System (ADS)
Abbaspour, Mohsen
2011-11-01
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.
NASA Astrophysics Data System (ADS)
Turi, László; Borgis, Daniel
2002-10-01
A new electron-water molecule pseudopotential is developed and tested in the present paper. The formal development of the potential is based on our earlier quantum mechanical model calculations of the excess electronic states of the electron-water molecule system [Turi et al., J. Chem. Phys. 114, 7805 (2001)]. Although the new pseudopotential has a very simple analytical form containing only nine adjustable parameters, it reproduces the exact eigenvalue of the excess state and the electron density of the smooth pseudo-wave function in the static-exchange limit. Of the individual potential energy terms, one can extract the exact electrostatic, the local repulsion and, as the remaining part, the local exchange potentials. The polarization term is added to the potential a posteriori. The most important feature of the potential is that the repulsive core region of the potential is finite and relatively narrow. This property leads to the non-negligible penetration of the excess electron in the core. The attractive wells of the potential also appear significantly closer to the nuclei than in previous pseudopotentials. The new pseudopotential is tested in quantum molecular dynamics simulations of a ground-state excess electron in a water bath. Whereas the basic features of the equilibrium hydrated electron are similar to those predicted in earlier simulations, important quantitative details are significantly improved relative to available experimental data. In particular, the simulations reproduce the equilibrium ground state energy and the optical absorption spectrum quite well. The differences of the present pseudopotential from previous works are also manifested in the more diffuse ground-state electron distribution and the more compact solvation structure. Further structural and dynamical consequences of the application of the new pseudopotential are analyzed in detail.
Vashishta, Priya; Kalia, Rajiv K.; Nakano, Aiichiro; Rino, Jose Pedro
2011-01-01
An effective interatomic interaction potential for AlN is proposed. The potential consists of two-body and three-body covalent interactions. The two-body potential includes steric repulsions due to atomic sizes, Coulomb interactions resulting from charge transfer between atoms, charge-induced dipole-interactions due to the electronic polarizability of ions, and induced dipole–dipole (van der Waals) interactions. The covalent characters of the Al–N–Al and N–Al–N bonds are described by the three-body potential. The proposed three-body interaction potential is a modification of the Stillinger–Weber form proposed to describe Si. Using the molecular dynamics method, the interaction potential is used to study structural, elastic, and dynamical properties of crystalline and amorphous states of AlN for several densities and temperatures. The structural energy for wurtzite (2H) structure has the lowest energy, followed zinc-blende and rock-salt (RS) structures. The pressure for the structural transformation from wurtzite-to-RS from the common tangent is found to be 24 GPa. For AlN in the wurtzite phase, our computed elastic constants ( C{sub 11} , C{sub 12} , C{sub 13} , C{sub 33} , C{sub 44} , and C{sub 66} ), melting temperature, vibrational density-of-states, and specific heat agree well with the experiments. Predictions are made for the elastic constant as a function of density for the crystalline and amorphous phase. Structural correlations, such as pair distribution function and neutron and x-ray static structure factors are calculated for the amorphous and liquid state.
Ping, Tan Ai; Hoe, Yeak Su
2014-07-10
Typically, short range potential only depends on neighbouring atoms and its parameters function can be categorized into bond stretching, angle bending and bond rotation potential. In this paper, we present our work called Angle Bending (AB) potential, whereas AB potential is the extension of our previous work namely Bond Stretching (BS) potential. Basically, potential will tend to zero after truncated region, potential in specific region can be represented by different piecewise polynomial. We proposed the AB piecewise potential which is possible to solve a system involving three atoms. AB potential able to handle the potential of covalent bonds for three atoms as well as two atoms cases due to its degeneracy properties. Continuity for the piecewise polynomial has been enforced by coupling with penalty methods. There are still plenty of improvement spaces for this AB potential. The improvement for three atoms AB potential will be studied and further modified into torsional potential which are the ongoing current research.
NASA Astrophysics Data System (ADS)
Kang, Hongbo; Zhang, Yuwen; Yang, Mo
2011-06-01
Mechanism of heat conduction in copper-argon nanofluids is studied by molecular dynamics simulation and the thermal conductivity was obtained using the Green-Kubo method. While the interatomic potential between argon atoms is described using the well-known Lennard-Jones (L-J) potential, a more accurate embedded atom method (EAM) potential is used in describing the interatomic interaction between copper atoms. It is found that the heat current autocorrelation function obtained using L-J potential to describe the copper-copper interatomic interaction fluctuates periodically due to periodic oscillation of the instantaneous microscopic heat fluxes. Thermal conductivities of nanofluids using EAM potentials were calculated with different volume fractions but the same nanoparticle size. The results show that thermal conductivity of nanofluids are almost a linear function of the volume fraction and slightly higher than the results predicted by the conventional effective media theory for a well-dispersed solution. A solid-like base fluid liquid layer with a thickness of 0.6 nm was found in the simulation and this layer is believed to account for the small discrepancy between the results of MD simulation and the conventional effective media theory.
Quantum molecular Dynamics Ronnie Kosloff
Kosloff, Ronnie
Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew University, Jerusalem Israel. · Lecture 6: · Time dependent Quantum Molecular Dynamics #12;#12;State #12;Quantum molecular Dynamics Ronnie Kosloff The Fritz Haber Center for Molecular Dynamics Hebrew
Larcher, G; Tran, H; Schwell, M; Chelin, P; Landsheere, X; Hartmann, J-M; Hu, S-M
2014-02-28
Room temperature absorption spectra of various transitions of pure CO2 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 CO2 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 CO2 transitions are almost independent of the rotational quantum number of the considered lines. PMID:24588170
Accelerating Fermionic Molecular Dynamics
M. A. Clark; A. D. Kennedy
2004-09-22
We consider how to accelerate fermionic molecular dynamics algorithms by introducing n pseudofermion fields coupled with the nth root of the fermionic kernel. This reduces the maximum pseudofermionic force, and thus allows a larger molecular dynamics integration step size without hitting an instability in the integrator.
NASA Astrophysics Data System (ADS)
Boisse, J.; Domain, C.; Becquart, C. S.
2014-12-01
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.
Noy, Karin; Kalisman, Nir; Keasar, Chen
2008-01-01
Background The structural stability of peptides in solution strongly affects their binding affinities and specificities. Thus, in peptide biotechnology, an increase in the structural stability is often desirable. The present work combines two orthogonal computational techniques, Molecular Dynamics and a knowledge-based potential, for the prediction of structural stability of short peptides (< 20 residues) in solution. Results We tested the new approach on four families of short ?-hairpin peptides: TrpZip, MBH, bhpW and EPO, whose structural stabilities have been experimentally measured in previous studies. For all four families, both computational techniques show considerable correlation (r > 0.65) with the experimentally measured stabilities. The consensus of the two techniques shows higher correlation (r > 0.82). Conclusion Our results suggest a prediction scheme that can be used to estimate the relative structural stability within a peptide family. We discuss the applicability of this predictive approach for in-silico screening of combinatorial peptide libraries. PMID:18510728
NASA Astrophysics Data System (ADS)
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems.
Fu, Yao; Song, Jeong-Hoon
2014-08-01
Hardy stress definition has been restricted to pair potentials and embedded-atom method potentials due to the basic assumptions in the derivation of a symmetric microscopic stress tensor. Force decomposition required in the Hardy stress expression becomes obscure for multi-body potentials. In this work, we demonstrate the invariance of the Hardy stress expression for a polymer system modeled with multi-body interatomic potentials including up to four atoms interaction, by applying central force decomposition of the atomic force. The balance of momentum has been demonstrated to be valid theoretically and tested under various numerical simulation conditions. The validity of momentum conservation justifies the extension of Hardy stress expression to multi-body potential systems. Computed Hardy stress has been observed to converge to the virial stress of the system with increasing spatial averaging volume. This work provides a feasible and reliable linkage between the atomistic and continuum scales for multi-body potential systems. PMID:25106571
Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
2015-01-01
The zoonotic disease brucellosis, a chronic condition in humans affecting renal and cardiac systems and causing osteoarthritis, is caused by Brucella, a genus of Gram-negative, facultative, intracellular pathogens. The mode of transmission and the virulence of the pathogens are still enigmatic. Transcription regulatory elements, such as rho proteins, play an important role in the termination of transcription and/or the selection of genes in Brucella. Adverse effects of the transcription inhibitors play a key role in the non-successive transcription challenges faced by the pathogens. In the investigation presented here, we computationally predicted the transcription termination factor rho (TtFRho) inhibitors against Brucella melitensis 16M via a structure-based method. In view the unknown nature of its crystal structure, we constructed a robust three-dimensional homology model of TtFRho’s structure by comparative modeling with the crystal structure of the Escherichia coli TtFRho (Protein Data Bank ID: 1PVO) as a template in MODELLER (v 9.10). The modeled structure was optimized by applying a molecular dynamics simulation for 2 ns with the CHARMM (Chemistry at HARvard Macromolecular Mechanics) 27 force field in NAMD (NAnoscale Molecular Dynamics program; v 2.9) and then evaluated by calculating the stereochemical quality of the protein. The flexible docking for the interaction phenomenon of the template consists of ligand-related inhibitor molecules from the ZINC (ZINC Is Not Commercial) database using a structure-based virtual screening strategy against minimized TtFRho. Docking simulations revealed two inhibitors compounds – ZINC24934545 and ZINC72319544 – that showed high binding affinity among 2,829 drug analogs that bind with key active-site residues; these residues are considered for protein-ligand binding and unbinding pathways via steered molecular dynamics simulations. Arg215 in the model plays an important role in the stability of the protein-ligand complex via a hydrogen bonding interaction by aromatic-? contacts, and the ADMET (absorption, distribution, metabolism, and excretion) analysis of best leads indicate nontoxic in nature with good potential for drug development. PMID:25848225
Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
2015-01-01
The zoonotic disease brucellosis, a chronic condition in humans affecting renal and cardiac systems and causing osteoarthritis, is caused by Brucella, a genus of Gram-negative, facultative, intracellular pathogens. The mode of transmission and the virulence of the pathogens are still enigmatic. Transcription regulatory elements, such as rho proteins, play an important role in the termination of transcription and/or the selection of genes in Brucella. Adverse effects of the transcription inhibitors play a key role in the non-successive transcription challenges faced by the pathogens. In the investigation presented here, we computationally predicted the transcription termination factor rho (TtFRho) inhibitors against Brucella melitensis 16M via a structure-based method. In view the unknown nature of its crystal structure, we constructed a robust three-dimensional homology model of TtFRho's structure by comparative modeling with the crystal structure of the Escherichia coli TtFRho (Protein Data Bank ID: 1PVO) as a template in MODELLER (v 9.10). The modeled structure was optimized by applying a molecular dynamics simulation for 2 ns with the CHARMM (Chemistry at HARvard Macromolecular Mechanics) 27 force field in NAMD (NAnoscale Molecular Dynamics program; v 2.9) and then evaluated by calculating the stereochemical quality of the protein. The flexible docking for the interaction phenomenon of the template consists of ligand-related inhibitor molecules from the ZINC (ZINC Is Not Commercial) database using a structure-based virtual screening strategy against minimized TtFRho. Docking simulations revealed two inhibitors compounds - ZINC24934545 and ZINC72319544 - that showed high binding affinity among 2,829 drug analogs that bind with key active-site residues; these residues are considered for protein-ligand binding and unbinding pathways via steered molecular dynamics simulations. Arg215 in the model plays an important role in the stability of the protein-ligand complex via a hydrogen bonding interaction by aromatic-? contacts, and the ADMET (absorption, distribution, metabolism, and excretion) analysis of best leads indicate nontoxic in nature with good potential for drug development. PMID:25848225
Yongfeng Zhang; Paul C. Millett; Michael Tonks
2011-10-01
This paper presents an interatomic potential for modeling of He defects and bubbles in body-centered-cubic (BCC) Mo. We utilize three existing framework: the Finnis-Sinclair (FS) potential for Mo-Mo, the Effective-Medium-Theory (EMT) for He-Mo, and the Hartree-Fock-Dispersion (HFD) potential for He-He interactions. The energetics of He defects and the diffusivity of He interstitial givens by the present potential agree well with ab initio calculations and experimental measurements. Furthermore, in agreement with theoretical prediction, it is shown that the introduction of He gas suppresses the surface diffusivity of BCC Mo, which decays exponentially with increasing He pressure acting on the free surface. The decay constant, with is correlated with the characteristic interaction volume for He-Mo, is close to the atomic volume of BCC Mo. This suppression effect is important to understand the mobility of small gas bubbles.
Molecular modeling of hydrate-clathrates via ab initio, cell potential, and dynamic methods
Anderson, Brian, Ph. D. Massachusetts Institute of Technology
2005-01-01
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 ...
Nonequilibrium molecular dynamics
Hoover, W.G. . Dept. of Applied Science Lawrence Livermore National Lab., CA )
1990-11-01
The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. 14 refs., 8 figs.
Molecular dynamics simulation of sputtering from a cylindrical track: EAM versus pair potentials
Zhigilei, Leonid V.
by energetic particle bom- bardment are performed for a gold target represented with a many-body embedded atom of earlier simulations performed with pair potentials have a general character and are not sensitive the spike model by integration of the thermal evaporation over time and surface area, predict a roughly
Martin Frank; Peter Gutbrod; Chokri Hassayoun; Claus-W. von der Lieth
2003-01-01
Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions
Lee, EokKyun
Lyapunov instability of rigid diatomic molecules via diatomic potential molecular dynamics Oyeon-dimensonal fluids composed of rigid diatomic molecules. The Lyapunov spectra are obtained for 18 rigid diatomic diatomic molecules are often described by hard dumbbells in shape, interacting with the so-called diatomic
Molecular electrostatic potentials by systematic molecular fragmentation
Reid, David M.; Collins, Michael A.
2013-11-14
A simple method is presented for estimating the molecular electrostatic potential in and around molecules using systematic molecular fragmentation. This approach estimates the potential directly from the electron density. The accuracy of the method is established for a set of organic molecules and ions. The utility of the approach is demonstrated by estimating the binding energy of a water molecule in an internal cavity in the protein ubiquitin.
Molecular dynamics simulations
Tomas Hansson; Chris Oostenbrink; WilfredF van Gunsteren
2002-01-01
Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible. Simulations aid our understanding of biochemical processes and give a dynamic dimension to structural
Alcaraz, Olga; Bitrián, Vicente; Trullàs, Joaquim
2011-01-01
The structure of molten AgCl, AgI, and their eutectic mixture Ag(Cl(0.43)I(0.57)) is studied by means of molecular dynamics simulations of polarizable ion model potentials. The corresponding static coherent structure factors reproduce quite well the available neutron scattering data. The qualitative behavior of the simulated partial structure factors and radial distribution functions for molten AgCl and AgI is that predicted by the reverse Monte Carlo modeling of the experimental data. The AgI results are also in qualitative agreement with those calculated from ab initio molecular dynamics. PMID:21219005
Hideki Tanaka; Hidekazu Touhara; Koichiro Nakanishi; Nobuatsu Watanabe
1984-01-01
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
Singh, Satendra; Sablok, Gaurav; Farmer, Rohit; Singh, Atul Kumar; Gautam, Budhayash; Kumar, Sunil
2013-01-01
In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5_TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10 ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was -0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (-13.0 Kcal/Mol) and a log P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. PMID:24073401
Singh, Satendra; Singh, Atul Kumar; Gautam, Budhayash
2013-01-01
In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5_TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10?ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was ?0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (?13.0?Kcal/Mol) and a log?P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. PMID:24073401
Molecular Dynamics Analysis Toolchest
a powerful means for studying the structure and dynamics of fairly large molecular systems. Theoretical information can be extracted. MD simulation packages usually come with some minimal set of analysis tools or allow for the users to add on their own analysis module
Pahari, Swagata; Choudhury, Chandan Kumar; Pandey, Prithvi Raj; More, Minal; Venkatnathan, Arun; Roy, Sudip
2012-06-21
Phosphoric acid doped polybenzimidazole is promising electrolyte membranes for high temperature (100 °C and above) fuel cells. Proton conduction is governed by the amount of phosphoric acid content in the polymer membrane. In this present work, we perform molecular dynamics simulations on phosphoric acid doped 2-phenyl-1H,1'H-5,5'-bibenzo[d]imidazole (monomer unit of polybenzimidazole) to characterize the structural and dynamical properties at varying phosphoric acid content and temperature. From the structural analysis, we have predicted the arrangement of the phosphoric acids, formation of H-bonds in the system, and the contribution of different atoms toward H-bonding. We have also examined the stacking of 2-phenyl-1H,1'H-5,5'-bibenzo[d]imidazole molecules and how their arrangement changes with the increasing amount of PA in the system with the help of cluster analysis. From the molecular dynamics simulation conducted at different temperatures and phosphoric acid doping level, we have predicted the diffusion of phosphoric acid and monomer. As a dynamic quantity, we have also calculated ring flipping of the imidazole ring of the monomer. PMID:22651825
Multiscale reactive molecular dynamics
NASA Astrophysics Data System (ADS)
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-12-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.
Multiscale reactive molecular dynamics
Knight, Chris; Lindberg, Gerrick E.; Voth, Gregory A.
2012-01-01
Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system. PMID:23249062
Interactive molecular dynamics
Schroeder, Daniel V
2015-01-01
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in HTML5 and JavaScript for running within any modern Web browser, is provided as an online supplement.
Wen, Rui; Rahn, Björn; Magnussen, Olaf M
2015-05-11
Room-temperature ionic liquids are of great current interest for electrochemical applications in material and energy science. Essential for understanding the electrochemical reactivity of these systems are detailed data on the structure and dynamics of the interfaces between these compounds and metal electrodes, which distinctly differ from those in traditional electrolytes. In situ studies are presented of Au(111) electrodes in 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([BMP][TFSA]) by high-speed scanning tunneling microscopy (video-STM). [BMP][TFSA] is one of the best-understood air and water stable ionic liquids. The measurements provide direct insights into the potential-dependent molecular arrangement and surface dynamics of adsorbed [BMP](+) cations in the innermost layer on the negatively charged Au electrode surface. In particular, two distinct subsequent transitions in the adlayer structure and lateral mobility are observed with decreasing potential. PMID:25913869
N, Nagasundaram; Zhu, Hailong; Liu, Jiming; V, Karthick; C, George Priya Doss; Chakraborty, Chiranjib; Chen, Luonan
2015-01-01
The cyclin-dependent kinase 4 (CDK4)-cyclin D1 complex plays a crucial role in the transition from the G1 phase to S phase of the cell cycle. Among the CDKs, CDK4 is one of the genes most frequently affected by somatic genetic variations that are associated with various forms of cancer. Thus, because the abnormal function of the CDK4-cyclin D1 protein complex might play a vital role in causing cancer, CDK4 can be considered a genetically validated therapeutic target. In this study, we used a systematic, integrated computational approach to identify deleterious nsSNPs and predict their effects on protein-protein (CDK4-cyclin D1) and protein-ligand (CDK4-flavopiridol) interactions. This analysis resulted in the identification of possible inhibitors of mutant CDK4 proteins that bind the conformations induced by deleterious nsSNPs. Using computational prediction methods, we identified five nsSNPs as highly deleterious: R24C, Y180H, A205T, R210P, and R246C. From molecular docking and molecular dynamic studies, we observed that these deleterious nsSNPs affected CDK4-cyclin D1 and CDK4-flavopiridol interactions. Furthermore, in a virtual screening approach, the drug 5_7_DIHYDROXY_ 2_ (3_4_5_TRI HYDROXYPHENYL) _4H_CHROMEN_ 4_ONE displayed good binding affinity for proteins with the mutations R24C or R246C, the drug diosmin displayed good binding affinity for the protein with the mutation Y180H, and the drug rutin displayed good binding affinity for proteins with the mutations A205T and R210P. Overall, this computational investigation of the CDK4 gene highlights the link between genetic variation and biological phenomena in human cancer and aids in the discovery of molecularly targeted therapies for personalized treatment. PMID:26252490
Jiang, Ludi; Zhang, Xianbao; Chen, Xi; He, Yusu; Qiao, Liansheng; Zhang, Yanling; Li, Gongyu; Xiang, Yuhong
2015-01-01
The metabotropic glutamate subtype 1 (mGluR1), a member of the metabotropic glutamate receptors, is a therapeutic target for neurological disorders. However, due to the lower subtype selectivity of mGluR1 orthosteric compounds, a new targeted strategy, known as allosteric modulators research, is needed for the treatment of mGluR1-related diseases. Recently, the structure of the seven-transmembrane domain (7TMD) of mGluR1 has been solved, which reveals the binding site of allosteric modulators and provides an opportunity for future subtype-selectivity drug design. In this study, a series of computer-aided drug design methods were utilized to discover potential mGluR1 negative allosteric modulators (NAMs). Pharmacophore models were constructed based on three different structure types of mGluR1 NAMs. After validation using the built-in parameters and test set, the optimal pharmacophore model of each structure type was selected and utilized as a query to screen the Traditional Chinese Medicine Database (TCMD). Then, three different hit lists of compounds were obtained. Molecular docking was used based on the latest crystal structure of mGluR1-7TMD to further filter these hits. As a compound with high QFIT and LibDock Score was preferred, a total of 30 compounds were retained. MD simulation was utilized to confirm the stability of potential compounds binding. From the computational results, thesinine-4'-O-?-d-glucoside, nigrolineaxanthone-P and nodakenin might exhibit negative allosteric moderating effects on mGluR1. This paper indicates the applicability of molecular simulation technologies for discovering potential natural mGluR1 NAMs from Chinese herbs. PMID:26184151
Stochastic Event-Driven Molecular Dynamics
Aleksandar Donev; Alejandro L. Garcia; Berni J. Alder
2008-01-01
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. SEDMD combines event-driven molecular dynamics (EDMD) with the Direct Simulation Monte Carlo (DSMC) method. The polymers are represented as chains of hard-spheres tethered by square wells and interact with the solvent particles with hard-core potentials. The algorithm uses EDMD for
NASA Astrophysics Data System (ADS)
Palacio, Juan Carlos Castro; Rubayo-Soneira, Jesús; Lombardi, Andrea; Aquilanti, Vincenzo
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 cage radius and the radial distribution function for the ground and excited states have been calculated for various orientations of the molecular axis with respect the Kr atom matrix with the NO molecule treated as a rigid rotor. The ab initio PESs, considered in previous work, seem to be too repulsive when compared with potentials fitted to spectroscopic data, and this is more evident for the first Ryberg state than for the ground state, where effects of potential anisotropy are less important. The first shell response shows a relative increase, up to sim10%, of the excited state equilibrium radius with respect to that of the ground state, while experiments indicate that such an increase should be less than 5%. The kinetic energy power spectrum method, presented in a previous work, has been applied to the total kinetic energy T(t) and to two characteristic quantities of the hyperspherical mode analysis, the hyperradial energy Trho(t) and the grand angular energy TLambda(t) for NO molecular axis orientations of 67° and 90°, respectively, which represent the cases of the largest and smallest lattice distortions in the radial distribution function (RDF) of the atoms in the matrix for the excited state. The band structures of the calculated frequency spectra reveal a blue shift with respect to the case of the isotropic potentials used previously, and this is connected to the different lattice equilibrium structures for 67° and 90° directions.
Appendix F Molecular Dynamics F.1 Introduction
Goddard III, William A.
269 Appendix F Molecular Dynamics F.1 Introduction In this chapter, we deal with the theories is the Lagrangian equation of motion d dt@L @ _qk = @L @qk F.1 where the Lagrangian function Lq; _q is de ned in terms of kinetic and potential energies L = K ,V F.2 F.2 NVE Dynamics For an isolated system, we have
Molecular Dynamics Calculations
NASA Technical Reports Server (NTRS)
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two 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.
NASA Astrophysics Data System (ADS)
Kallinteris, G. C.; Papanicolaou, N. I.; Evangelakis, G. A.; Papaconstantopoulos, D. A.
1997-01-01
We present an alternate approach to parametrizing the expression for the total energy of solids within the second-moment approximation (SMA) of the tight-binding theory. In order to obtain the necessary parameters, we do not use the experimental values of the lattice constant, the elastic constants, and the cohesive energy, but we fit to the total energy obtained from first-principles augmented-plane-wave calculations as a function of volume. In addition, we shift the total-energy graphs uniformly so that at the minimum they give the experimental value of the cohesive energy. We have applied the above methodology to perform molecular-dynamics simulations of the noble metals. For Cu and Ag our results for vacancy formation energies, relaxed surface energies, phonon spectra, and various temperature-dependent quantities are of comparable accuracy to those found by the standard SMA, which is based on fitting to several measured data. However, our approach does not seem to work as well for Au.
NASA Astrophysics Data System (ADS)
Tanaka, Hideki; Nakanishi, Koichiro; Touhara, Hidekazu
1985-06-01
Molecular dynamics calculation (MD) has been carried out for an aqueous solution of urea at 298.15 K and with experimental density value at ordinary pressure by the use of constant temperature technique developed previously. The total number of molecules is 216, of which 17 are urea. The mole fraction of urea in the solution is thus 0.078. For water-water and water-urea interactions, the MCY potential and previously determined potential have been used. A new urea-urea pair potential is determined by ab initio LCAO SCF calculations for more than 750 different dimer configurations with an STO-3G basis set and subsequent multiparameter optimization of the MO data to a 12-6-3-1 potential energy function. The MD calculation is extended up to 76 000 time steps and final 44 000 time steps (17.6 ps) are used to calculate both static and dynamic properties. Among other information, the following results are important and interesting: (1) Urea molecules exhibit appreciable self-association, (2) such association is possible with strong hydrogen bondings and this is in sharp contrast with the association of t-butanol through hydrophobic interaction studied previously, (3) there is no evidence that urea destroys structure of water, and (4) the decrease of self-diffusion coefficient of water in urea solution is appreciably smaller than that in the case of t-butanol solution.
Molecular Dynamics (MD) Gas Module
NSDL National Science Digital Library
Iacovella, Christopher R.
2007-12-10
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.
Meng, Qingyong; Chen, Jun; Zhang, Dong H
2015-09-14
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300?K ? T ? 1000?K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures. PMID:26373990
Jono, Ryota; Tateyama, Yoshitaka; Yamashita, Koichi
2015-10-28
We demonstrate the redox potential calculation relative to the normal hydrogen electrode (NHE) in nonaqueous solution using a density functional theory-based molecular dynamics (DFT-MD) simulation. The calculation of the NHE in nonaqueous solution consists of two processes: the first step is the equilibrated simulation for a proton in nonaqueous solution to determine the space for inserting a proton in solution, and the second step is the thermodynamic integration method to calculate the solvation energy of the proton in the nonaqueous solution. In this work, we apply the method for a cation and an anion, i.e., copper(ii)/copper(i) and iodine/iodide in acetonitrile solution, and show that the errors in the calculated redox potential from experiments are within 0.21 V. PMID:26412242
NASA Astrophysics Data System (ADS)
Meng, Qingyong; Chen, Jun; Zhang, Dong H.
2015-09-01
The ring polymer molecular dynamics (RPMD) calculations are performed to calculate rate constants for the title reaction on the recently constructed potential energy surface based on permutation invariant polynomial (PIP) neural-network (NN) fitting [J. Li et al., J. Chem. Phys. 142, 204302 (2015)]. By inspecting convergence, 16 beads are used in computing free-energy barriers at 300 K ? T ? 1000 K, while different numbers of beads are used for transmission coefficients. The present RPMD rates are in excellent agreement with quantum rates computed on the same potential energy surface, as well as with the experimental measurements, demonstrating further that the RPMD is capable of producing accurate rates for polyatomic chemical reactions even at rather low temperatures.
NASA Astrophysics Data System (ADS)
Yang, Xu-qiu; Zhai, Peng-cheng; Liu, Li-sheng; Chen, Gang; Zhang, Qing-jie
2014-06-01
Molecular dynamics simulations have been performed to investigate the effect of nanometer-size pores on the phonon conductivity of single-crystal bulk CoSb3. The cylindrical pores are uniformly distributed along two vertical principal crystallographic directions of a square lattice. Because pore diameter and porosity are two key factors that could affect the performance of the materials, they were varied individually in the ranges a 0-6 a 0 and 0.1-5%, respectively, where a 0 is the lattice constant of CoSb3. The simulation results indicate that the phonon conductivity of nanoporous CoSb3 is significantly lower than that of no-pore CoSb3. The reduction of phonon conductivity in this simulation was consistent with the ballistic-diffusive microscopic effective medium model, demonstrating the ballistic character of phonon transport when the phonon mean-free-path is comparable with or larger than the pore size. Reducing pore diameter or increasing porosity are alternative means of effective reduction of the thermal conductivity of CoSb3. These results are expected to provide a useful basis for the design of high-performance skutterudites.
Molecular Dynamics Simulations to Study Protein Folding and Unfolding
Caflisch, Amedeo
32 Molecular Dynamics Simulations to Study Protein Folding and Unfolding Amedeo Caflisch] and books [57]. 32.2 Molecular Dynamics Simulations of Peptides and Proteins 32.2.1 Folding of Structured for the potential energy (force field) and to solve the time- discretized Newton equation of motion (molecular
Larcher, G.; Tran, H. Schwell, M.; Chelin, P.; Landsheere, X.; Hartmann, J.-M.; Hu, S.-M.
2014-02-28
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.
Lowell W. Ungar; Norbert F. Scherer; Gregory A. Voth
1997-01-01
Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photo- induced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground
NASA Astrophysics Data System (ADS)
Goldstein, Sheldon; Struyve, Ward
2015-01-01
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
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.
Nonadiabatic Molecular Dynamics with Trajectories
NASA Astrophysics Data System (ADS)
Tavernelli, Ivano
2012-02-01
In the mixed quantum-classical description of molecular systems, only the quantum character of the electronic degrees of freedom is considered while the nuclear motion is treated at a classical level. In the adiabatic case, this picture corresponds to the Born-Oppenheimer limit where the nuclei move as point charges on the potential energy surface (PES) associated with a given electronic state. Despite the success of this approximation, many physical and chemical processes do not fall in the regime where nuclei and electrons can be considered decoupled. In particular, most photoreactions pass through regions of the PES in which electron-nuclear quantum interference effects are sizeable and often crucial for a correct description of the phenomena. Recently, we have developed a trajectory-based nonadiabatic molecular dynamics scheme that describes the nuclear wavepacket as an ensemble of particles following classical trajectories on PESs derived from time-dependent density functional theory (TDDFT) [1]. The method is based on Tully's fewest switches trajectories surface hopping (TSH) where the nonadiabatic coupling elements between the different potential energy surfaces are computed on-the-fly as functionals of the ground state electron density or, equivalently, of the corresponding Kohn-Sham orbitals [2]. Here, we present the theoretical fundamentals of our approach together with an extension that allows for the direct coupling of the dynamics to an external electromagnetic field [3] as well as to the external potential generated by the environment (solvent effects) [4]. The method is applied to the study of the photodissociation dynamics of simple molecules in gas phase and to the description of the fast excited state dynamics of molecules in solution (in particular Ruthenium (II) tris(bipyridine) in water). [4pt] [1] E. Tapavicza, I. Tavernelli, U. Rothlisberger, Phys. Rev. Lett., 98, (2007) 023001. [0pt] [2] Tavernelli I.; Tapavicza E.; Rothlisberger U., J. Chem. Phys., 130, (2009) 124107; Tavernelli I., Curchod B.F.E., Rothlisberger U., J. Chem. Phys., 131, (2009) 196101; Tavernelli I., Curchod B.F.E., Laktionov A., Rothlisberger U., J. Chem. Phys., 133, (2010) 194104. [0pt] [3] Tavernelli I., Curchod B.F.E., Rothlisberger U., Phys. Rev. A, 81, (2010) 052508. [0pt] [4] Tavernelli I., Curchod B.F.E., Rothlisberger U., Phys. Chem., accepted 2011.
NASA Astrophysics Data System (ADS)
Zhang, Yan; Lin, Hai
2009-05-01
Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6?-hydrogen abstraction and the 6?-d1-testosterone 6?-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.
Iyengar, Srinivasan S.
Quantum Wavepacket Ab-initio Molecular Dynamics Formalism for Calculating Electron Transport through molecular wires. The simultaneous dynamics of electrons and nuclei in the wire is coupled. · Due to the difference in potential between the two electrodes, electrons tunnel through the molecular
Ab Initio Molecular Dynamics Simulations of Biologically Relevant Systems
Alessandra Magistrate; Paolo Carloni
2005-01-01
Ab initio (Car-Parrinello) molecular dynamics (AIMD) simulations [1] are increasingly used to investigate structural, dynamical, energetic and electronic properties of biomolecules. At opposite to classical MD simulations, in this approach the underlying potential energy surface is calculated directly from first-principles. This leads to a parameter free molecular dynamics, where interatomic forces are not empirically derived, but are evaluated from electronic
NASA Astrophysics Data System (ADS)
Barone, Luciano Maria; Simonazzi, Riccardo; Tenenbaum, Alexander
1995-09-01
We have studied portability, efficiency and accuracy of a standard Molecular Dynamics simulation on the SIMD parallel computer APE100. Computing speed performance and physical system size range have been analyzed and compared with those of a conventional computer. Short range and long range potentials have been considered, and the comparative advantage of different simulation approaches has been assessed. For long range potentials, APE turns out to be faster than a conventional computer; large systems can be conveniently simulated using either the cloning approach (up to ˜ 10 5 particles) or a domain decomposition with the systolic method. In the case of short range potentials and systems with diffusion (like a liquid), APE is convenient only when using a large number of processors. In a special case (a crystal without diffusion), a specific domain decomposition technique with frames makes APE advantageous for intermediate and large systems. Using the latter technique we have studied in detail the effect of different numerical error sources, and compared the accuracy of APE with that of a conventional computer.
Molecular dynamics simulations of biomolecules
J. Andrew McCammon; Martin Karplus
2002-01-01
Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin
Brela, Mateusz Z; Wójcik, Marek J; Boczar, Marek; Witek, ?ukasz; Yasuda, Mitsuru; Ozaki, Yukihiro
2015-06-25
We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid. PMID:26028251
NASA Astrophysics Data System (ADS)
Tanaka, H.; Touhara, Hidekazu; Nakanishi, Koichiro; Watanabe, Nobuatsu
1984-05-01
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.
Pradhan, Dibyabhaba; Priyadarshini, Vani; Munikumar, Manne; Swargam, Sandeep; Umamaheswari, Amineni; Bitla, Aparna
2014-01-01
Leptospira interrogans, a Gram-negative bacterial pathogen is the main cause of human leptospirosis. Lipid A is a highly immunoreactive endotoxic center of lipopolysaccharide (LPS) that anchors LPS into the outer membrane of Leptospira. Discovery of compounds inhibiting lipid-A biosynthetic pathway would be promising for dissolving the structural integrity of membrane leading to cell lysis and death of Leptospira. LpxC, a unique enzyme of lipid-A biosynthetic pathway was identified as common drug target of Leptospira. Herein, homology modeling, docking, and molecular dynamics (MD) simulations were employed to discover potential inhibitors of LpxC. A reliable tertiary structure of LpxC in complex with inhibitor BB-78485 was constructed in Modeller 9v8. A data-set of BB-78485 structural analogs were docked with LpxC in Maestro v9.2 virtual screening workflow, which implements three stage Glide docking protocol. Twelve lead molecules with better XP Gscore compared to BB-78485 were proposed as potential inhibitors of LpxC. Para-(benzoyl)-phenylalanine - that showed lowest XP Gscore (-10.35?kcal/mol) - was predicted to have best binding affinity towards LpxC. MD simulations were performed for LpxC and para-(benzoyl)-phenylalanine docking complex in Desmond v3.0. Trajectory analysis showed the docking complex and inter-molecular interactions was stable throughout the entire production part of MD simulations. The results indicate para-(benzoyl)-phenylalanine as a potent drug molecule against leptospirosis. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:10. PMID:23383626
State-dependent molecular dynamics.
Yang, Ciann-Dong; Weng, Hung-Jen
2014-01-01
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
Dynamic molecular graphs: "hopping" structures.
Cortés-Guzmán, Fernando; Rocha-Rinza, Tomas; Guevara-Vela, José Manuel; Cuevas, Gabriel; Gómez, Rosa María
2014-05-01
This work aims to contribute to the discussion about the suitability of bond paths and bond-critical points as indicators of chemical bonding defined within the theoretical framework of the quantum theory of atoms in molecules. For this purpose, we consider the temporal evolution of the molecular structure of [Fe{C(CH2 )3 }(CO)3 ] throughout Born-Oppenheimer molecular dynamics (BOMD), which illustrates the changing behaviour of the molecular graph (MG) of an electronic system. Several MGs with significant lifespans are observed across the BOMD simulations. The bond paths between the trimethylenemethane and the metallic core are uninterruptedly formed and broken. This situation is reminiscent of a "hopping" ligand over the iron atom. The molecular graph wherein the bonding between trimethylenemethane and the iron atom takes place only by means of the tertiary carbon atom has the longest lifespan of all the considered structures, which is consistent with the MG found by X-ray diffraction experiments and quantum chemical calculations. In contrast, the ?(4) complex predicted by molecular-orbital theory has an extremely brief lifetime. The lifespan of different molecular structures is related to bond descriptors on the basis of the topology of the electron density such as the ellipticities at the Fe?CH2 bond-critical points and electron delocalisation indices. This work also proposes the concept of a dynamic molecular graph composed of the different structures found throughout the BOMD trajectories in analogy to a resonance hybrid of Lewis structures. It is our hope that the notion of dynamic molecular graphs will prove useful in the discussion of electronic systems, in particular for those in which analysis on the basis of static structures leads to controversial conclusions. PMID:24692252
We have explored the degree to which an intermolecular potential for the explosive hexahydro-1,3,5-trinitro-1,3,5-s-triazine (RDX) is transferable for predictions of crystal structures (within the approximation of rigid molecules) of a similar chemical system,in this case, polymo...
Simon, Aude; Iftner, Christophe; Mascetti, Joëlle; Spiegelman, Fernand
2015-03-19
The present theoretical study aims at investigating the effects of an argon matrix on the structures, energetics, dynamics, and infrared (IR) spectra of small water clusters (H2O)n (n = 1-6). The potential energy surface is obtained from a hybrid self-consistent charge density functional-based tight binding/force-field approach (SCC-DFTB/FF) in which the water clusters are treated at the SCC-DFTB level and the matrix is modeled at the FF level by a cluster consisting of ?340 Ar atoms with a face centered cubic (fcc) structure, namely (H2O)n/Ar. With respect to a pure FF scheme, this allows a quantum description of the molecular system embedded in the matrix, along with all-atom geometry optimization and molecular dynamics (MD) simulations of the (H2O)n/Ar system. Finite-temperature IR spectra are derived from the MD simulations. The SCC-DFTB/FF scheme is first benchmarked on (H2O)Arn clusters against correlated wave function results and DFT calculations performed in the present work, and against FF data available in the literature. Regarding (H2O)n/Ar systems, the geometries of the water clusters are found to adapt to the fcc environment, possibly leading to intermolecular distortion and matrix perturbation. Several energetical quantities are estimated to characterize the water clusters in the matrix. In the particular case of the water hexamer, substitution and insertion energies for the prism, bag, and cage are found to be lower than that for the 6-member ring isomer. Finite-temperature MD simulations show that the water monomer has a quasifree rotation motion at 13 K, in agreement with experimental data. In the case of the water dimer, the only large-amplitude motion is a distortion-rotation intermolecular motion, whereas only vibration motions around the nuclei equilibrium positions are observed for clusters with larger sizes. Regarding the IR spectra, we find that the matrix environment leads to redshifts of the stretching modes and almost no shift of the bending modes. This is in agreement with experimental data. Furthermore, in the case of the water monomer and dimer, the magnitudes of the computed shifts are in fair agreement with the experimental values. The complex case of the water hexamer, which presents several low-energy isomers, is discussed. PMID:25650885
Hall, G.E.; Prrese, J.M.; Sears, T.J.; Weston, R.E.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution high-sensitivity laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular flee radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule.
SEARS,T.J.; HALL,G.E.; PRESES,J.M.; WESTON,R.E.,JR.
1999-06-09
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions involving short-lived chemical intermediates and their properties. High-resolution, high-sensitivity, laser absorption methods are augmented by high temperature flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals in chemical systems. The experimental work is supported by theoretical and computational work using time-dependent quantum wavepacket calculations that provide insights into energy flow between the vibrational modes of the molecule. The work of group members Fockenberg and Muckerman is described in separate abstracts of this volume.
Mapping molecular dynamics computations to hypercubes
Lakamsani, Vamsee Krishna
1993-01-01
This thesis proposes an approach for systematic modeling, mapping and performance analysis of a Grand Challenge application problem in computational biology called Molecular Dynamics Simulation of Proteins. Molecular Dynamics (MD) is an important...
Efficient Compression of Molecular Dynamics Trajectory Files
Gain, James
Efficient Compression of Molecular Dynamics Trajectory Files Patrick Marais,*[a] Julian Kenwood properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: ``interframe'' predictors, which exploit
Grand canonical Molecular Dynamics Simulations
Fritsch, S; Junghans, C; Ciccotti, G; Site, L Delle; Kremer, K
2011-01-01
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.
Novel methods for molecular dynamics simulations.
Elber, R
1996-04-01
In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced. PMID:8728657
Molecular dynamics investigation of nanoscale cavitation dynamics
NASA Astrophysics Data System (ADS)
Sasikumar, Kiran; Keblinski, Pawel
2014-12-01
We use molecular dynamics simulations to investigate the cavitation dynamics around intensely heated solid nanoparticles immersed in a model Lennard-Jones fluid. Specifically, we study the temporal evolution of vapor nanobubbles that form around the solid nanoparticles heated over ps time scale and provide a detail description of the following vapor formation and collapse. For 8 nm diameter nanoparticles we observe the formation of vapor bubbles when the liquid temperature 0.5-1 nm away from the nanoparticle surface reaches ˜90% of the critical temperature, which is consistent with the onset of spinodal decomposition. The peak heat flux from the hot solid to the surrounding liquid at the bubble formation threshold is ˜20 times higher than the corresponding steady state critical heat flux. Detailed analysis of the bubble dynamics indicates adiabatic formation followed by an isothermal final stage of growth and isothermal collapse.
Molecular dynamics investigation of nanoscale cavitation dynamics.
Sasikumar, Kiran; Keblinski, Pawel
2014-12-21
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
Wick, Collin D.; Chang, Tsun-Mei; Dang, Liem X.
2010-11-25
Molecular dynamics simulations with many-body interactions were carried out to understand the bulk and interfacial absorption of gases in 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF4). A new polarizable molecular model was developed for BMIMBF4, which was found to give the correct liquid density, but also had good agreement with experiment for its surface tension and X-ray reflectivity. The potential of mean force of CO2 and SO2 were calculated across the air-BMIMBF4 interface, and the bulk free energies were calculated with the free energy perturbation method. A new polarizable model was also developed for CO2. The air-BMIMBF4 interface had enhanced BMIM density, which was mostly related to its butyl group, followed by enhanced BF4 density a few angstroms towards the liquid bulk. The density profiles were observed to exhibit oscillations between high BMIM and BF4 density, indicating the presence of surface layering induced by the interface. The potential of mean force for CO2 and SO2 showed more negative free energies in regions of enhanced BF4 density, while more positive free energies in regions of high BMIM density. Moreover, these gases showed free energy minimums at the interface, where the BMIM alkyl groups were found to be most prevalent. Our results show the importance of ionic liquid interfacial ordering for understanding gas solvation in them. This work was supported by the US Department of Energy Basic Energy Sciences' Chemical Sciences, Geosciences & Biosciences Division. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.
2015-01-01
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
Molecular electrostatic potential as a graph.
Daza, Edgar E; Maza, Julio; Torres, Raul
2013-06-01
We present several procedures to represent molecular electrostatic potential as a graph, based on the pattern of critical points and their neighborhood relations. This representation is used for the molecular electrostatic comparison, which is reduced to a comparison of tree-type graphs. Several methods to compare trees are also presented. The applications of this algorithm to compare and classify molecules through their electrostatic potential are illustrated. PMID:23700998
NMR investigations of molecular dynamics
NASA Astrophysics Data System (ADS)
Palmer, Arthur
2011-03-01
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.
Better, Cheaper, Faster Molecular Dynamics
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.
Hybrid molecular dynamics simulations of living filaments
NASA Astrophysics Data System (ADS)
Caby, Mathieu; Hardas, Priscilla; Ramachandran, Sanoop; Ryckaert, Jean-Paul
2012-03-01
We propose a hybrid molecular dynamics/multi-particle collision dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte Carlo scheme to deal with single monomer addition (polymerization) or removal (depolymerization), satisfying the detailed balance condition within a proper statistical mechanical framework. This model of filaments, based on the wormlike chain, aims to represent equilibrium polymers with distinct reaction rates at both ends, such as self-assembled adenosine diphosphate-actin filaments in the absence of adenosine triphosphate (ATP) hydrolysis and other proteins. We report the distribution of filament lengths and the corresponding dynamical fluctuations on an equilibrium trajectory. Potential generalizations of this method to include irreversible steps like ATP-actin hydrolysis are discussed.
Potential formulation of sleep dynamics
NASA Astrophysics Data System (ADS)
Phillips, A. J. K.; Robinson, P. A.
2009-02-01
A physiologically based model of the mechanisms that control the human sleep-wake cycle is formulated in terms of an equivalent nonconservative mechanical potential. The potential is analytically simplified and reduced to a quartic two-well potential, matching the bifurcation structure of the original model. This yields a dynamics-based model that is analytically simpler and has fewer parameters than the original model, allowing easier fitting to experimental data. This model is first demonstrated to semiquantitatively match the dynamics of the physiologically based model from which it is derived, and is then fitted directly to a set of experimentally derived criteria. These criteria place rigorous constraints on the parameter values, and within these constraints the model is shown to reproduce normal sleep-wake dynamics and recovery from sleep deprivation. Furthermore, this approach enables insights into the dynamics by direct analogies to phenomena in well studied mechanical systems. These include the relation between friction in the mechanical system and the timecourse of neurotransmitter action, and the possible relation between stochastic resonance and napping behavior. The model derived here also serves as a platform for future investigations of sleep-wake phenomena from a dynamical perspective.
Potential formulation of sleep dynamics.
Phillips, A J K; Robinson, P A
2009-02-01
A physiologically based model of the mechanisms that control the human sleep-wake cycle is formulated in terms of an equivalent nonconservative mechanical potential. The potential is analytically simplified and reduced to a quartic two-well potential, matching the bifurcation structure of the original model. This yields a dynamics-based model that is analytically simpler and has fewer parameters than the original model, allowing easier fitting to experimental data. This model is first demonstrated to semiquantitatively match the dynamics of the physiologically based model from which it is derived, and is then fitted directly to a set of experimentally derived criteria. These criteria place rigorous constraints on the parameter values, and within these constraints the model is shown to reproduce normal sleep-wake dynamics and recovery from sleep deprivation. Furthermore, this approach enables insights into the dynamics by direct analogies to phenomena in well studied mechanical systems. These include the relation between friction in the mechanical system and the timecourse of neurotransmitter action, and the possible relation between stochastic resonance and napping behavior. The model derived here also serves as a platform for future investigations of sleep-wake phenomena from a dynamical perspective. PMID:19391784
A system for interactive molecular dynamics simulation
John E. Stone; Justin Gullingsrud; Klaus Schulten
2001-01-01
We have implemented a system termed Interactive Molecu- lar Dynamics (IMD), which permits manipulation of mole- cules in molecular dynamics simulations with real-time force feedback and graphical display. Communication is achieved through an e cient socket connection between the visual- ization program (VMD) and a molecular dynamics program (NAMD) running on single or multiple machines. A natural force feedback interface
Protein-Folding Dynamics: Overview of Molecular
Zhigilei, Leonid V.
Protein-Folding Dynamics: Overview of Molecular Simulation Techniques Harold A. Scheraga, Mey models, force fields Abstract Molecular dynamics (MD) is an invaluable tool with which to study protein folding in silico. Although just a few years ago the dynamic be- havior of a protein molecule could
A concurrent multiscale micromorphic molecular dynamics
NASA Astrophysics Data System (ADS)
Li, Shaofan; Tong, Qi
2015-04-01
In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.
On the blackhole dynamic potentials
Koustubh Ajit Kabe
2010-03-08
In the following paper, certain blackhole dynamic potentials have been developed definitively on the lines of classical thermodynamics. These potentials have been refined in view of the small differences in the equations of the laws of blackhole dynamics as given by Bekenstein and those of thermodynamics. Nine fundamental blackhole dynamical relations have been developed akin to the four fundamental thermodynamic relations of Maxwell. The specific heats and have been defined. For a blackhole, these quantities are negative. The equation has been obtained as an application of these fundamental relations. Time reversible processes observing constancy of surface gravity are considered and an equation connecting the internal energy of the blackhole, the additional available energy defined as the first free energy function, and the surface gravity, has been obtained. Finally as a further application of the fundamental relations, it has been proved for a homogeneous gravitational field in blackhole spacetimes that . This is dubbed as the homogeneous fluid approximation in context of the blackholes.
On the blackhole dynamic potentials
Kabe, Koustubh Ajit
2010-01-01
In the following paper, certain blackhole dynamic potentials have been developed definitively on the lines of classical thermodynamics. These potentials have been refined in view of the small differences in the equations of the laws of blackhole dynamics as given by Bekenstein and those of thermodynamics. Nine fundamental blackhole dynamical relations have been developed akin to the four fundamental thermodynamic relations of Maxwell. The specific heats and have been defined. For a blackhole, these quantities are negative. The equation has been obtained as an application of these fundamental relations. Time reversible processes observing constancy of surface gravity are considered and an equation connecting the internal energy of the blackhole, the additional available energy defined as the first free energy function, and the surface gravity, has been obtained. Finally as a further application of the fundamental relations, it has been proved for a homogeneous gravitational field in blackhole spacetimes that ....
Radiation in molecular dynamic simulations
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M
2008-10-13
Hot dense radiative (HDR) plasmas common to Inertial Confinement Fusion (ICF) and stellar interiors have high temperature (a few hundred eV to tens of keV), high density (tens to hundreds of g/cc) and high pressure (hundreds of Megabars to thousands of Gigabars). Typically, such plasmas undergo collisional, radiative, atomic and possibly thermonuclear processes. In order to describe HDR plasmas, computational physicists in ICF and astrophysics use atomic-scale microphysical models implemented in various simulation codes. Experimental validation of the models used to describe HDR plasmas are difficult to perform. Direct Numerical Simulation (DNS) of the many-body interactions of plasmas is a promising approach to model validation but, previous work either relies on the collisionless approximation or ignores radiation. We present a new numerical simulation technique to address a currently unsolved problem: the extension of molecular dynamics to collisional plasmas including emission and absorption of radiation. The new technique passes a key test: it relaxes to a blackbody spectrum for a plasma in local thermodynamic equilibrium. This new tool also provides a method for assessing the accuracy of energy and momentum exchange models in hot dense plasmas. As an example, we simulate the evolution of non-equilibrium electron, ion, and radiation temperatures for a hydrogen plasma using the new molecular dynamics simulation capability.
Molecular dynamics of interface rupture
NASA Technical Reports Server (NTRS)
Koplik, Joel; Banavar, Jayanth R.
1993-01-01
Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.
Unified approach for molecular dynamics and density-functional theory
R. Car; M. Parrinello
1985-01-01
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
Application of optimal prediction to molecular dynamics
Barber IV, John Letherman
2004-12-01
Optimal prediction is a general system reduction technique for large sets of differential equations. In this method, which was devised by Chorin, Hald, Kast, Kupferman, and Levy, a projection operator formalism is used to construct a smaller system of equations governing the dynamics of a subset of the original degrees of freedom. This reduced system consists of an effective Hamiltonian dynamics, augmented by an integral memory term and a random noise term. Molecular dynamics is a method for simulating large systems of interacting fluid particles. In this thesis, I construct a formalism for applying optimal prediction to molecular dynamics, producing reduced systems from which the properties of the original system can be recovered. These reduced systems require significantly less computational time than the original system. I initially consider first-order optimal prediction, in which the memory and noise terms are neglected. I construct a pair approximation to the renormalized potential, and ignore three-particle and higher interactions. This produces a reduced system that correctly reproduces static properties of the original system, such as energy and pressure, at low-to-moderate densities. However, it fails to capture dynamical quantities, such as autocorrelation functions. I next derive a short-memory approximation, in which the memory term is represented as a linear frictional force with configuration-dependent coefficients. This allows the use of a Fokker-Planck equation to show that, in this regime, the noise is {delta}-correlated in time. This linear friction model reproduces not only the static properties of the original system, but also the autocorrelation functions of dynamical variables.
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
Donald Hamelberg; John Mongan; J. Andrew McCammon
2004-01-01
Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential
Molecular dynamics simulation of condensed-phase chiral molecular propellers.
Yoneya, M; Tabe, Y; Yokoyama, H
2010-07-01
Molecular dynamics simulations were performed for an axial-chiral liquid crystalline (LC) monolayer under trans-monolayer gas flow. The rotational dynamics of the monolayer chiral LC molecule along its long-molecular axis were analyzed at the molecular level. We found a precise correspondence between the flow-driven molecular rotation direction and molecular chirality as well as between the rotation direction and the trans-monolayer flow direction. The rotational direction exactly corresponded to what was expected in the proposed chiral molecular propeller model (Tabe, Y.; Yokoyama, H. Nat. Mater. 2003, 2, 806). Among the four trans-monolayer gas species we investigated, we found argon to be the most efficient at driving the chiral molecular propeller and helium the least efficient. PMID:20536201
Molecular dynamics simulations of nanostructures
NASA Astrophysics Data System (ADS)
Yuan, Zaoshi
This dissertation is focused on multimillion-atom molecular dynamics (MD) simulations of nanoscale materials. In the past decade, nanoscale materials have made significant commercial impacts, which will potentially lead to the next industrial revolution. The interest lies in the novel and promising features nanoscale materials exhibit due to their confined sizes. However, not all novel behaviors are understood or controllable. Many uncontrollable parameters, e.g. defects and dangling bonds, are known to hinder the performance of nanodevices. Solutions to these problems rely on our understanding of fundamental elements in nanoscience: isolated individual nanostructures and their assemblies. In this dissertation, we will address atomistic foundations of several problems of technological importance in nanoscience. Specifically, three basic problems are discussed: (1) embrittlement of nanocrystalline metal; (2) novel thermo-mechanical behaviors of nanowires (NWs); and (3) planar defect generation in NWs. With a scalable algorithm implemented on massively parallel computing platforms and various data mining methods, MD simulations can provide valuable insights into these problems. An essential role of sulfur segregation-induced amorphization of crystalline nickel was recently discovered experimentally, but the atomistic mechanism of the amorphization remains unexplained. Our MD simulations reveal that the large steric size of sulfur impurity causes strong sulfur-sulfur interaction mediated by lattice distortion, which leads to amorphization near the percolation threshold at the sulfur-sulfur network in nickel crystal. The generality of the mechanism due to the percolation of an impurity network is further confirmed by a model binary system. In our study of novel behaviors of semiconductor NWs, MD simulations construct a rich size-temperature `phase diagram' for the mechanical response of a zinc-oxide NW under tension. For smaller diameters and higher temperatures, novel 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.
Buckybomb: Reactive Molecular Dynamics Simulation.
Chaban, Vitaly V; Fileti, Eudes Eterno; Prezhdo, Oleg V
2015-03-01
Energetic materials, such as explosives, propellants, and pyrotechnics, are widely used in civilian and military applications. Nanoscale explosives represent a special group because of the high density of energetic covalent bonds. The reactive molecular dynamics (ReaxFF) study of nitrofullerene decomposition reported here provides a detailed chemical mechanism of explosion of a nanoscale carbon material. Upon initial heating, C60(NO2)12 disintegrates, increasing temperature and pressure by thousands of Kelvins and bars within tens of picoseconds. The explosion starts with NO2 group isomerization into C-O-N-O, followed by emission of NO molecules and formation of CO groups on the buckyball surface. NO oxidizes into NO2, and C60 falls apart, liberating CO2. At the highest temperatures, CO2 gives rise to diatomic carbon. The study shows that the initiation temperature and released energy depend strongly on the chemical composition and density of the material. PMID:26262672
A multicell molecular dynamics method
NASA Astrophysics Data System (ADS)
Kandemir, Ilyas
1999-09-01
Kinetic theory has been an important field of interest for researchers in the 20th century. According to kinetic theory, a gas is considered as an ensemble of particles, molecules. As the computational capabilities increased in the second half of the century, computer simulations of this theory have attracted scientists. Molecular Dynamics (MD) constitutes a major simulation technique that has been used extensively. However, the number of particles (N) in MD simulations is limited by the computational capabilities. Studies with large N, which are needed in many fluid dynamics problems and in low Knudsen number simulations, require large memory and fast computers. Therefore, they are expensive and usually time consuming. New techniques that help on these issues are needed. In this study a multi-cell method and associated vectorial search technique are developed in response to that need. In the multi-cell approach, the whole computational region is divided into subregions, cells, and calculations for distant molecular interactions are greatly avoided. However, since molecules are allowed to switch cells no real collision is lost, and results are identical with the single-region approach The computational speed for a given number of interactions in the multicell method is approximately proportional to N whereas it was N2 in single-region approach. A multi-cell MD computer program is developed to examine the hard sphere gases. Low Kn MD simulations of some basic transport phenomena are made, filling a gap in the previous MD studies. One dimensional heat transfer, Couette flow, and binary diffusion problems are examined. Behavior of the gas near the walls and the factors that affect mean free path are studied. The transport coefficient variations and property profiles deduced in the heat transfer and Couette flow studies are probably definitive for this class of gas.
RedMD--reduced molecular dynamics package.
Górecki, Adam; Szypowski, Marcin; D?ugosz, Maciej; Trylska, Joanna
2009-11-15
We developed a software package (RedMD) to perform molecular dynamics simulations and normal mode analysis of reduced models of proteins, nucleic acids, and their complexes. With RedMD one can perform molecular dynamics simulations in a microcanonical ensemble, with Berendsen and Langevin thermostats, and with Brownian dynamics. We provide force field and topology generators which are based on the one-bead per residue/nucleotide elastic network model and its extensions. The user can change the force field parameters with the command line options that are passed to generators. Also, the generators can be modified, for example, to add new potential energy functions. Normal mode analysis tool is available for elastic or anisotropic network models. The program is written in C and C++ languages and the structure/topology of a molecule is based on an XML format. OpenMP technology for shared-memory architectures was used for code parallelization. The code is distributed under GNU public licence and available at http://bionano.icm.edu.pl/software/. PMID:19247989
Welch, David A.; Mehdi, Beata L.; Hatchell, Hanna J.; Faller, Roland; Evans, James E.; Browning, Nigel D.
2015-03-25
Understanding the fundamental processes taking place at the electrode-electrolyte interface in batteries will play a key role in the development of next generation energy storage technologies. One of the most fundamental aspects of the electrode-electrolyte interface is the electrical double layer (EDL). Given the recent development of high spatial resolution in-situ electrochemical cells for scanning transmission electron microscopy (STEM), there now exists the possibility that we can directly observe the formation and dynamics of the EDL. In this paper we predict electrolyte structure within the EDL using classical models and atomistic Molecular Dynamics (MD) simulations. The MD simulations show thatmore »the classical models fail to accurately reproduce concentration profiles that exist within the electrolyte. It is thus suggested that MD must be used in order to accurately predict STEM images of the electrode-electrolyte interface. Using MD and image simulations together for a high contrast electrolyte (the high atomic number CsCl electrolyte), it is determined that, for a smooth interface, concentration profiles within the EDL should be visible experimentally. When normal experimental parameters such as rough interfaces and low-Z electrolytes (like those used in Li-ion batteries) are considered, observation of the EDL appears to be more difficult.« less
Replica Exchange Statistical Temperature Molecular Dynamics Jaegil Kim,*,
Straub, John E.
simulations of complex fluids and biomolecules, molecular dynamics (MD) is preferable to MC, dueReplica Exchange Statistical Temperature Molecular Dynamics Algorithm Jaegil Kim,*, John E. Straub ABSTRACT: The replica exchange statistical temperature molecular dynamics (RESTMD) algorithm is presented
Identification of Allosteric Mechanisms in Thrombin through Molecular Dynamics Simulations /
Gasper, Paul M.
2013-01-01
molecular dynamics: A promising and efficient simulation method for biomolecules.Molecular dynamics (MD) simulation, an established method for investigating the internal motions of biomolecules,molecular trajectories provide a wealth of information on the internal dynamics of biomolecules
From Molecular Dynamics to Conformational Dynamics in Drug Design
PETER DEUFLHARD
2002-01-01
Abstract Computational drug design studies molecular recognitionin thevir tual lab. The arising Hamiltonian dynamics,is knownto be chaotic and ill-conditioned already after picoseconds(= 10 -12 seconds), whereas timesof pharmaceutical,interestare in themilliseconds (= 10 -3 sec onds)up,tominutes.,Classical molecular dynamics,with long term trajectory computation gives,at best, information about timeand statistical ensemble averages. The present paper surveysa recent new modelling approach called conformational dynamics,
Hele, Timothy J H; Muolo, Andrea; Althorpe, Stuart C
2015-01-01
We recently obtained a quantum-Boltzmann-conserving classical dynamics by making a single change to the derivation of the `Classical Wigner' approximation. Here, we show that the further approximation of this `Matsubara dynamics' gives rise to two popular heuristic methods for treating quantum Boltzmann time-correlation functions: centroid molecular dynamics (CMD) and ring-polymer molecular dynamics (RPMD). We show that CMD is a mean-field approximation to Matsubara dynamics, obtained by discarding (classical) fluctuations around the centroid, and that RPMD is the result of discarding a term in the Matsubara Liouvillian which shifts the frequencies of these fluctuations. These findings are consistent with previous numerical results, and give explicit formulae for the terms that CMD and RPMD leave out.
First principles molecular dynamics without self-consistent field optimization
Souvatzis, Petros; Niklasson, Anders M. N.
2014-01-28
We present a first principles molecular dynamics approach that is based on time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] in the limit of vanishing self-consistent field optimization. The optimization-free dynamics keeps the computational cost to a minimum and typically provides molecular trajectories that closely follow the exact Born-Oppenheimer potential energy surface. Only one single diagonalization and Hamiltonian (or Fockian) construction are required in each integration time step. The proposed dynamics is derived for a general free-energy potential surface valid at finite electronic temperatures within hybrid density functional theory. Even in the event of irregular functional behavior that may cause a dynamical instability, the optimization-free limit represents a natural starting guess for force calculations that may require a more elaborate iterative electronic ground state optimization. Our optimization-free dynamics thus represents a flexible theoretical framework for a broad and general class of ab initio molecular dynamics simulations.
Thermal transpiration: A molecular dynamics study
NASA Astrophysics Data System (ADS)
T, Joe Francis; Sathian, Sarith P.
2014-12-01
Thermal transpiration is a phenomenon where fluid molecules move from the cold end towards the hot end of a channel under the influence of longitudinal temperature gradient alone. Although the phenomenon of thermal transpiration is observed at rarefied gas conditions in macro systems, the phenomenon can occur at atmospheric pressure if the characteristic dimensions of the channel is less than 100 nm. The flow through these nanosized channels is characterized by the free molecular flow regimes and continuum theory is inadequate to describe the flow. Thus a non-continuum method like molecular dynamics (MD) is necessary to study such phenomenon. In the present work, MD simulations were carried out to investigate the occurance of thermal transpiration in copper and platinum nanochannels at atmospheric pressure conditions. The mean pressure of argon gas confined inside the nano channels was maintained around 1 bar. The channel height is maintained at 2nm. The argon atoms interact with each other and with the wall atoms through the Lennard-Jones potential. The wall atoms are modelled using an EAM potential. Further, separate simulations were carried out where a Harmonic potential is used for the atom-atom interaction in the platinum channel. A thermally insulating wall was introduced between the low and high temperature regions and those wall atoms interact with fluid atoms through a repulsive potential. A reduced cut off radius were used to achieve this. Thermal creep is induced by applying a temperature gradient along the channel wall. It was found that flow developed in the direction of the increasing temperature gradient of the wall. An increase in the volumetric flux was observed as the length of the cold and the hot regions of the wall were increased. The effect of temperature gradient and the wall-fluid interaction strength on the flow parameters have been studied to understand the phenomenon better.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
Turi, László
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of the non-cavity type model. Relaxation associated with cavity collapse presents, however, unique dynamical signatures.
Hydration dynamics in water clusters via quantum molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Turi, László
2014-05-01
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.
Hydration dynamics in water clusters via quantum molecular dynamics simulations.
Turi, László
2014-05-28
We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of the non-cavity type model. Relaxation associated with cavity collapse presents, however, unique dynamical signatures. PMID:24880290
Sobolewski, Emil; O?dziej, Stanis?aw; Wi?niewska, Marta; Liwo, Adam; Makowski, Mariusz
2012-01-01
By means of molecular dynamics simulations of 15 pairs of molecules selected to model the interactions of nonpolar, nonpolar and polar, nonpolar and charged, polar, and polar and charged side chains in water, we determined the potentials of mean force (PMFs) of pairs of interacting molecules in water as functions of distance between the interacting particles or their distance and orientations at three temperatures: 283 K, 323 K and 373 K, respectively. The systems were found to fall into the following four categories as far as the temperature dependence of the potential of mean force is concerned: (i) pairs, for which association is entropy-driven (ii) pairs, for which association is energy-driven, (iii), pairs of positively-charged solute molecules, for which association is energy-driven with unfavorable entropy change, and (iv) the remaining systems for which temperature dependence is weak. For each pair of PMFs entropic and energetic contributions have been discussed. PMID:22475198
Oxidation modeling by means of molecular dynamics
NASA Astrophysics Data System (ADS)
Soontrapa, Chaiyod
Oxidation modeling is normally engineered to study systems at macroscopic scales, mostly in analytical forms based on diffusion theories. The associated time scale is usually in months, days, or minutes, and the length scale is in the order of microns. In this dissertation, oxidation modeling is performed at atomistic scale with the time and length scales in picoseconds and angstroms, respectively, using molecular dynamics. Molecular dynamics simulations generate trajectories of each atom or particle in a system according to the laws of physics. Studying oxidations under the atomistic point of view can offer new insights on atomic behaviors and influencing factors in oxidation mechanisms. This dissertation focuses on modeling dynamic behaviors of liquid lead, oxygen, and iron. Lead is used as a coolant in nuclear reactors due to its excellent physical properties such as high boiling point and neutron transparency. Nevertheless, liquid lead is very corrosive to iron, the main structural material in reactors. As lead diffuses along grain boundaries and other faults in iron crystals, iron lattices become brittle. In addition, oxygen dissolving in liquid lead causes another problem. Too much oxygen promotes undesired compound formations of lead oxide, typically known as slags, which hinder the coolant flow. However, when only traces of oxygen are present in this lead-iron system, protective iron oxide layers form and help preventing further ingress of liquid lead. This dissertation provides a new approach in modeling oxidations, using the Generalized Reduced Gradient (GRG) method in minimizing the potential energy of a metal/metal oxide system. The approach is then applied to model iron oxidation in the form of magnetite. Finally, a system consisting of liquid lead, iron, and oxygen is studied under several scenarios.
SECOND-ORDER METHODS FOR THE OPTIMIZATION OF MOLECULAR POTENTIAL
Helgaker, Trygve
-9784 USA The optimization of ab initio Born-Oppenheimer potential energy surfaces is an important subject of the molecular potential energy surface are an essential tool in studies of molecular structure and reactivitySECOND-ORDER METHODS FOR THE OPTIMIZATION OF MOLECULAR POTENTIAL ENERGY SURFACES 1 Introduction
Molecular Dynamics Simulations of Simple Liquids
ERIC Educational Resources Information Center
Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.
2004-01-01
An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.
Modeling the Hydrogen Bond within Molecular Dynamics
ERIC Educational Resources Information Center
Lykos, Peter
2004-01-01
The structure of a hydrogen bond is elucidated within the framework of molecular dynamics based on the model of Rahman and Stillinger (R-S) liquid water treatment. Thus, undergraduates are exposed to the powerful but simple use of classical mechanics to solid objects from a molecular viewpoint.
Molecular ions, Rydberg spectroscopy and dynamics
NASA Astrophysics Data System (ADS)
Jungen, Ch.
2015-01-01
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.
Multiple time step integrators in ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Luehr, Nathan; Markland, Thomas E.; Martínez, Todd J.
2014-02-01
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.
Multiple time step integrators in ab initio molecular dynamics
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
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.
Molecular dynamics simulations of calcium binding in gramicidin A
Turgut Ba?tu?; Serdar Kuyucak
2006-01-01
An important issue in molecular dynamics (MD) simulations of biomolecules is whether membrane proteins can be described using nonpolarizable force fields. To shed further light into this question, we study calcium ion binding and blocking of the gramicidin A channel which has not been investigated in MD simulations before. Potential of mean force calculations for calcium and potassium ions using
Molecular Dynamics Studies of Ion Permeation in VDAC
Rui, Huan; Lee, Kyu II; Pastor, Richard W.; Im, Wonpil
2011-02-02
, and the mechanisms underlying its electrophysiological properties, we performed a total of 1.77 ?s molecular dynamics simulations of human VDAC isoform 1 in DOPE/DOPC mixed bilayers in 1 M KCl solution with transmembrane potentials of 0, ±25, ±50, ±75, and ±100 m...
MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER OF CARBON NANOTUBES
Maruyama, Shigeo
MOLECULAR DYNAMICS SIMULATIONS OF HEAT TRANSFER OF CARBON NANOTUBES J. Shiomi, Y. Igarashi, Y-ku, Tokyo 113-8656, JAPAN Several heat transfer problems related to single-walled carbon nanotubes (SWNTs] is employed as the potential function between carbon and carbon within a nanotube. MD simulations of thermal
Investigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation
Investigating Wear Mechanisms of Alkylsilane Monolayers through Molecular Dynamics Simulation-1263182 iMoDELS project, Grant ACI-1047828 Motivation and Project Overview Future Work · Systematic obtained from the Optimized Potentials for Liquid Simulations all-atom (OPLS-AA) force field · Temperature
Laser Coulomb explosion imaging of molecular dynamics
NASA Astrophysics Data System (ADS)
Bocharova, Irina A.
2009-11-01
The goal of this dissertation project was to study the dynamics of nuclear motion in diatomic (H2, N2, O2, CO) and triatomic (CO2) molecules initiated by the ionization and/or excitation of these molecules with near-IR few-cycle laser pulses. This dynamics includes vibrational and rotational motion on the electronic potential surfaces of the molecules and their molecular ions. The experimental techniques used included the pump-probe approach, laser Coulomb explosion imaging and the COLTRIMS technique. The results are presented in four chapters. A study of rotational and vibrational nuclear dynamics in H2 and D2 molecules and ions initiated by 8 fs near-IR pulses is presented in Chapter 4. Transient alignment of the neutral molecules was observed and simulated; rotational frequency components contributing to the rotational wavepacket dynamics were recovered. Chapter 5 is dedicated to revealing the contribution of excited dissociative states of D2+ ions to the process of fragmentation by electron recollision. It was shown that it is possible to isolate the process of resonant excitation and estimate the individual contributions of the 2Sigmau+ and 2? u states. In Chapter 6 the subject of investigation is the nuclear dynamics of N2, O2 and CO molecules initiated by ionization of a neutral molecule by a short intense laser pulse. It was shown that the kinetic energy release of the Coulomb explosion fragments, measured as a function of the delay time between pump and probe pulses, reveals the behavior of nuclear wave packet evolution on electronic states of the molecular ions. It was shown that information on the dissociation and excitation pathways can be extracted from the experimental spectra and the relative contributions of particular electronic states can be estimated. Chapter 7 is focused on studying the fragmentation of CO2 following the interaction of this molecule with the laser field. The most important result of this study was that it presented direct experimental evidence of charge-resonant enhanced ionization (CREI), a phenomenon well-studied for diatomic molecules and predicted theoretically for triatomic molecules. The critical internuclear distance, the relevant ionic charge state and a pair of charge-resonant states responsible for the CREI were also found.
A Virtual Environment for Steered Molecular Dynamics
Jan F. Prins; Jan Hermans; Geoffrey Mann; Lars S. Nyland; Martin Simons
1999-01-01
A molecular dynamics simulation approximates the motion of atoms in a system of molecules over short intervals of simulated time, typically on the order of picoseconds to nanoseconds. Such simulations may run for days or weeks on a computer when used to investigate the dynamic behavior of small proteins in biological systems. By adding additional restraints, a simulation may be
Flexibility in Biomolecules: Beyond Molecular Dynamics
Michael Thorpe
2006-01-01
Molecular dynamics is unable to explore the conformations large protein complexes, viral capsids etc. Using Lagrange constraints for covalent bonds, hydrogen bonds, hydrophobic tethers, and van der Waals excluded volumes, Monte Carlo dynamics uses ghost templates to efficiently guide rigid clusters via the flexible joints between them. The generation a new protein conformation typically requires about 100 milliseconds CPU time.
Osmosis : a molecular dynamics computer simulation study
NASA Astrophysics Data System (ADS)
Lion, Thomas
Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..
Kapko, Vitaliy; Zhao, Zuofeng; Matyushov, Dmitry V; Austen Angell, C
2013-03-28
The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and?or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972)]--and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010)] that some object shapes find little advantage in self-assembly to ordered structures--meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004); A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004)] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003)] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005)] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers"--single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length?diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010)]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points T(m), liquidus temperatures T(l), and glass transition temperatures T(g), we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995)]." PMID:23556800
A Review of Wave Packet Molecular Dynamics
Paul E. Grabowski
2014-08-09
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.
Nonholonomic Hamiltonian Method for Molecular Dynamics Simulations of Reacting Shocks
NASA Astrophysics Data System (ADS)
Fahrenthold, Eric; Bass, Joseph
2015-06-01
Conventional molecular dynamics simulations of reacting shocks employ a holonomic Hamiltonian formulation: the breaking and forming of covalent bonds is described by potential functions. In general these potential functions: (a) are algebraically complex, (b) must satisfy strict smoothness requirements, and (c) contain many fitted parameters. In recent research the authors have developed a new noholonomic formulation of reacting molecular dynamics. In this formulation bond orders are determined by rate equations and the bonding-debonding process need not be described by differentiable functions. This simplifies the representation of complex chemistry and reduces the number of fitted model parameters. Example applications of the method show molecular level shock to detonation simulations in nitromethane and RDX. Research supported by the Defense Threat Reduction Agency.
Theoretical analysis of dynamic processes for interacting molecular motors
NASA Astrophysics Data System (ADS)
Teimouri, Hamid; Kolomeisky, Anatoly B.; Mehrabiani, Kareem
2015-02-01
Biological transport is supported by the collective dynamics of enzymatic molecules that are called motor proteins or molecular motors. Experiments suggest that motor proteins interact locally via short-range potentials. We investigate the fundamental role of these interactions by carrying out an analysis of a new class of totally asymmetric exclusion processes, in which interactions are accounted for in a thermodynamically consistent fashion. This allows us to explicitly connect microscopic features of motor proteins with their collective dynamic properties. A theoretical analysis that combines various mean-field calculations and computer simulations suggests that the dynamic properties of molecular motors strongly depend on the interactions, and that the correlations are stronger for interacting motor proteins. Surprisingly, it is found that there is an optimal strength of interactions (weak repulsion) that leads to a maximal particle flux. It is also argued that molecular motor transport is more sensitive to attractive interactions. Applications of these results for kinesin motor proteins are discussed.
Method of molecular dynamics in mechanics of deformable solids
NASA Astrophysics Data System (ADS)
Kiselev, S. P.
2014-05-01
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.
MolecularMolecular DynamicsDynamics Simulation of Shock WavesSimulation of Shock Waves
Wolberg, George
MolecularMolecular DynamicsDynamics Simulation of Shock WavesSimulation of Shock Waves Interacting Andreopoulos The City College of New York/CUNY #12;· The interaction of shock waves with gas-solid mixtures-scales. · The process of interaction of a shock wave with a surface involves a partial reflection of the shock
Emulating Molecular Orbitals and Electronic Dynamics with Ultracold Atoms
NASA Astrophysics Data System (ADS)
Lühmann, Dirk-Sören; Weitenberg, Christof; Sengstock, Klaus
2015-07-01
In recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly correlated phases and complex phenomena in solid-state systems. Here, we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated ? electron system with special regard to localization and spin order. The dynamical time scales of ultracold atom simulators are on the order of milliseconds, which allows for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated ? system of the artificial benzene molecule.
Molecular dynamics simulations of displacement cascades in metallic systems
NASA Astrophysics Data System (ADS)
Doan, N. V.; Tietze, H.
1995-08-01
We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature.
Molecular dynamics investigations of protein volumetric properties and electronic dynamics
NASA Astrophysics Data System (ADS)
Lockwood, Daren Mackay
Several theoretical and molecular dynamics investigations. of chemical and biological processes in solution are described. First, a statistical mechanical methodology is developed for evaluating excess volumetric properties of solvation. This methodology makes it possible to analyze volumetric properties in terms of the hydration shell model of solvation. The usefulness of the maximum entropy method for dealing with simulations with which significant statistical error is associated is explored. Second, this methodology is used to isolate additive contributions to the partial molar compressibilities of alcohols in aqueous solution. The magnitude of methyl and hydroxyl group contributions for methanol and ethanol are found to be the same for both solutes within statistical error. Further, the effect of each functional group on the solvent is found to be localized in the vicinity of that functional group, explaining the apparent independence of functional group contributions observed experimentally by other workers. For the potential functions employed, compressibilities calculated via classical molecular dynamics simulations are in best agreement with experiments performed at temperatures higher than those at which the simulations are performed. Finally , the effect of electronic decoherence on electron transfer rates in blue copper proteins is investigated. Electronic decoherence occurs as nuclear trajectories corresponding to alternative electronic states diverge from one another, and higher decoherence rates correspond to reduced direct electron transfer rates. A very short characteristic decoherence time of 2.4 fs is obtained for direct electron transfer between metal centers in ruthenated azurin. Protons in the aqueous solvent molecules have a large effect on the decoherence rate, underscoring the importance of treating the solvent molecules explicitly.
Considerations and Recent Advances in Molecular Dynamics Introduction
Considerations and Recent Advances in Molecular Dynamics Simon Ye Introduction Molecular dynamics simulations were first proposed in the 1950-60s as a method to study the motions of atoms at the molecular level. Today, the most prominent use of molecular dynamics is the study of biological molecules
Understanding Modularity in Molecular Networks Requires Dynamics
NSDL National Science Digital Library
Roger P. Alexander (Yale University; Program in Computational Biology and Bioinformatics REV)
2009-07-28
The era of genome sequencing has produced long lists of the molecular parts from which cellular machines are constructed. A fundamental goal in systems biology is to understand how cellular behavior emerges from the interaction in time and space of genetically encoded molecular parts, as well as nongenetically encoded small molecules. Networks provide a natural framework for the organization and quantitative representation of all the available data about molecular interactions. The structural and dynamic properties of molecular networks have been the subject of intense research. Despite major advances, bridging network structure to dynamics—and therefore to behavior—remains challenging. A key concept of modern engineering that recurs in the functional analysis of biological networks is modularity. Most approaches to molecular network analysis rely to some extent on the assumption that molecular networks are modular—that is, they are separable and can be studied to some degree in isolation. We describe recent advances in the analysis of modularity in biological networks, focusing on the increasing realization that a dynamic perspective is essential to grouping molecules into modules and determining their collective function.
Multifractal and complex network analyses of protein molecular dynamics
Zhou, Yuan-Wu; Yu, Zu-Guo; Zhao, Zhi-Qin; Anh, Vo
2014-01-01
Based on protein molecular dynamics, we analyze fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuations analysis (MF-DFA); and investigate the topological and multifractal properties of their visibility graph (complex network) representations. The energy terms of proteins we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. Results of MF-DFA show that these time series are multifractal. The numerical values of the exponent $h(2)$ of MF-DFA which is related to Hurst exponent $H$ show that the series of total energy and potential energy are non-stationary and anti-persistent; other kinds of time series are stationary and persistent apart from series of pressure which has the weakest memorability with $H\\approx 0.5$. Results of complex networks analysis based on visibility graph algorithm show that these visibility graphs ...
Nonisothermal gravitational segregation by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Galliéro, Guillaume; Montel, François
2008-10-01
In this work, a molecular dynamics algorithm is proposed to study the transient and the stationary state of gravitational segregation in simple fluid mixtures. Both isothermal and stable nonisothermal (where thermodiffusion occurs) cases have been studied. This approach is applied extensively on a simple fluid model: Lennard-Jones mixtures composed of species differing only in their masses. First, using isothermal binary equimolar mixtures, it is shown that the molecular dynamics simulations provide stationary results consistent with the thermodynamic modeling in various thermodynamic conditions and for different gravity fields. Next, in stable nonisothermal mixtures heated from below, it is shown that the gravitational segregation and the thermodiffusion process (Soret effect) have an opposite effect on the concentration profiles along the fluid column. Then, molecular dynamics simulations are performed on ternary and ten-component mixtures. For these multicomponent nonisothermal mixtures, results obtained emphasize the fact that the way the thermodiffusion is estimated should be done with care. In addition, for all nonisothermal configurations, the simulation results confirm that the thermodiffusion may have a non-negligible influence on the concentration profile in a petroleum reservoir. Finally, by analyzing the transient behavior during the molecular dynamics simulations, it is shown that the dynamic of the gravitational segregation is unambiguously controlled by the mass diffusion.
Nonisothermal gravitational segregation by molecular dynamics simulations.
Galliéro, Guillaume; Montel, François
2008-10-01
In this work, a molecular dynamics algorithm is proposed to study the transient and the stationary state of gravitational segregation in simple fluid mixtures. Both isothermal and stable nonisothermal (where thermodiffusion occurs) cases have been studied. This approach is applied extensively on a simple fluid model: Lennard-Jones mixtures composed of species differing only in their masses. First, using isothermal binary equimolar mixtures, it is shown that the molecular dynamics simulations provide stationary results consistent with the thermodynamic modeling in various thermodynamic conditions and for different gravity fields. Next, in stable nonisothermal mixtures heated from below, it is shown that the gravitational segregation and the thermodiffusion process (Soret effect) have an opposite effect on the concentration profiles along the fluid column. Then, molecular dynamics simulations are performed on ternary and ten-component mixtures. For these multicomponent nonisothermal mixtures, results obtained emphasize the fact that the way the thermodiffusion is estimated should be done with care. In addition, for all nonisothermal configurations, the simulation results confirm that the thermodiffusion may have a non-negligible influence on the concentration profile in a petroleum reservoir. Finally, by analyzing the transient behavior during the molecular dynamics simulations, it is shown that the dynamic of the gravitational segregation is unambiguously controlled by the mass diffusion. PMID:18999408
Kinetic theory molecular dynamics; numerical considerations
NASA Astrophysics Data System (ADS)
Michta, David; Surh, Michael; Graziani, Frank
2013-12-01
Typical numerical simulations of dense plasmas are limited by either an inability to treat the dynamical quantum evolution of the electrons or a difficulty with strongly-coupled ions. Yet these different physics problems are individually well-treated by particular approximations. Kinetic theory molecular dynamics (KTMD) is a hybrid approach that treats electrons via kinetic theory (KT) and ions with molecular dynamics (MD). We present a derivation suitable for classical plasmas and specialize to the Vlasov or mean-field case. In addition, we consider the limit of adiabatic electron dynamics, where the problem reduces to the Poisson-Boltzmann (PB) equations coupled to MD. An exploration of practical ways to implement KTMD within an existing MD framework. The initial goal is to develop computationally efficient solutions of the PB problem, suitable for large-scale PB or Thomas-Fermi MD simulations.
Molecular Dynamics Simulations of Alzheimer's ?-Amyloid Protofilaments
Nicolae-Viorel Buchete; Robert Tycko; Gerhard Hummer
2005-01-01
Filamentous amyloid aggregates are central to the pathology of Alzheimer's disease. We use all-atom molecular dynamics (MD) simu- lations with explicit solvent and multiple force fields to probe the structural stability and the conformational dynamics of several models of Alzheimer's b-amyloid fibril structures, for both wild-type and mutated amino acid sequences. The structural models are based on recent solid state
Molecular Dynamics Study of Phase Change of Water inside a Single-Walled Carbon Nanotube
Maruyama, Shigeo
The phase change of liquid water to ice crystal inside a single-walled carbon nanotube (SWNT) was studiedMolecular Dynamics Study of Phase Change of Water inside a Single-Walled Carbon Nanotube Shigeo with molecular dynamics simulations. Water molecules were modeled with SPC/E potential and carbon
(Quantum Molecular Dynamics Method) (Classical Molecular Dynamics Method)
Maruyama, Shigeo
) Tc* = 1.35 Tt* = 0.68 9) rc = 2.5 5.5 b. 6,10) SPC/E, TIP4P CC SPC/E (Extended Simple Lennard-Jones 9 3 Jorgenson TIP4P 12) 3 #12;HOH 2 SPC/E TIP4P TIP4P Jorgenson OPLS (optimized potential for liquid simulations) 13) CC (Carravetta-Clementi) 14) TIP4P (8) Lennard-Jones SPC/E, TIP4
Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz*
Heinz, Stefan
Molecular to fluid dynamics: The consequences of stochastic molecular motion Stefan Heinz) The derivation of fluid dynamic equations from molecular equations is considered. This is done on the basis equations. The stochastic model is used to derive fluid dynamic equations where the molecular stress tensor
Rational Prediction with Molecular Dynamics for Hit Identification
Nichols, Sara E; Swift, Robert V; Amaro, Rommie E
2012-01-01
Although the motions of proteins are fundamental for their function, for pragmatic reasons, the consideration of protein elasticity has traditionally been neglected in drug discovery and design. This review details protein motion, its relevance to biomolecular interactions and how it can be sampled using molecular dynamics simulations. Within this context, two major areas of research in structure-based prediction that can benefit from considering protein flexibility, binding site detection and molecular docking, are discussed. Basic classification metrics and statistical analysis techniques, which can facilitate performance analysis, are also reviewed. With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline. PMID:23110535
MDLab: A molecular dynamics simulation prototyping environment
Trevor M. Cickovski; Santanu Chatterjee; Jacob Wenger; Christopher R. Sweet; Jesús A. Izaguirre
2010-01-01
Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and ve- locities over a timestept. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep re- quired for propagation, and the expensive algorithm for computing pairwise
Molecular Dynamics Simulation of Vascular Network Formation
Triolo, Livio
Molecular Dynamics Simulation of Vascular Network Formation Paolo Butt`a1 , Fiammetta Cerreti1", Compendio Viminale, 00184 Roma, Italy 4 Dipartimento di Matematica, Universit`a di Roma "Tor Vergata", Via for the formation of the capillary blood vessel network. We describe a system of endothelial cells by means of two
Structural and dynamic properties of calcium aluminosilicate melts: A molecular dynamics study
NASA Astrophysics Data System (ADS)
Bouhadja, M.; Jakse, N.; Pasturel, A.
2013-06-01
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.
Molecular Dynamics Simulations of Graphene Oxide Frameworks
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
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.
C. Bussai; S. Hannongbua; S. Fritzsche; R. Haberlandt
2002-01-01
The silicalite-1\\/water potential function has been developed using quantum chemical calculations at the Hartree–Fock level using the 6-31G* basis sets. The silicalite-1 crystal structure is represented by three fragments, in which the chemical compositions are O10Si10H20,O30Si22H44 and O35Si29H58. Ab initio calculations have been performed for 1032 fragment–water configurations where water coordinates are generated inside the fragments. The intermolecular silicalite-1\\/water potentials
Molecular understanding of mutagenicity using potential energy methods
Broyde, S.; Shapiro, R.
1992-07-01
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.
Molecular dynamics studies of phase transition of KI clusters
NASA Astrophysics Data System (ADS)
Zhu, Xiao-lei; You, Xiao-zeng; Xiong, Ren-gen; Zhou, Zhihua
2001-07-01
Structural, energetic, and dynamics aspects of phase transitions of several KI clusters have been analyzed by molecular dynamics simulations. Born-Mayer-Huggins potential function was employed to reproduce melting and freezing when clusters are heated and cooled. Various diagnostic methods were applied to molecular dynamics simulations of heating and cooling stages including caloric curves, the Lindemann index, diffusion coefficients, and pair-correlation functions. Results demonstrate clusters of salt behave very differently from clusters of nonpolar molecule and melting temperatures decreased approximately linearly with the reciprocal of cluster radius, as expected according to conventional, attractive Reiss, Mirabel, and Whetten model. The melting temperature of bulk KI obtained by extrapolation is close to the experiment.
Shifted forces in molecular dynamics
Søren Toxvaerd; Jeppe C. Dyre
2011-02-03
Simulations involving the Lennard-Jones potential usually employ a cut-off at $r=2.5\\sigma$. This paper investigates the possibility of reducing the cut-off. Two different cut-off implementations are compared, the standard shifted potential cut-off and the less commonly used shifted forces cut-off. The first has correct forces below the cut-off, whereas the shifted forces cut-off modifies Newton's equations at all distances. The latter is nevertheless superior; we find that for most purposes realistic simulations may be obtained using a shifted-forces cut-off at $r=1.5\\sigma$, even though the pair force is here 30 times larger than at $r=2.5\\sigma$.
A molecular dynamics study on uranium–plutonium mixed nitride
Ken Kurosaki; Kimihiko Yano; Kazuhiro Yamada; Masayoshi Uno; Shinsuke Yamanaka
2001-01-01
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
A molecular dynamics study of barium meta-fluorozirconate glass
Y. Kawamoto; T. Horisaka; K. Hirao; N. Soga
1985-01-01
Molecular dynamics simulation was performed on barium meta-fluorozirconate, BaZrF6, glass by using the Born–Mayer–Huggins pair potential. The cumulative F coordination numbers and the F correlation functions of Zr and Ba ions revealed that, in the simulated BaZrF6 glass, the number and the mean distance of the nearest neighboring F were about eight at 2.12 A? for Zr ions and about
Molecular dynamics study of an aqueous SrClâ solution
E. Spohr; G. Palinkas; K. Heinzinger; P. Bopp; M. M. Probst
1988-01-01
A molecular dynamics simulation of a 1.1 m SrClâ solution was performed with an improved central force model for water at the experimental density at room temperature. The ion-water and ion-ion potentials were derived from ab initio calculations. The simulation extended over 4 ps at an average temperature of 298 K. The structural properties of the solution are discussed on
Molecular dynamics simulation studies of the mercury-water interface
Josef Böcker; Renat R. Nazmutdinov; Eckhard Spohr; Karl Heinzinger
1995-01-01
Molecular dynamics (MD) simulation studies of the mercury-water interface are presented. A slab of water molecules, about 25Åwide, confined by mercury phases, is investigated. A rigid water model and a flexible water model are used to describe the water-water interactions. Recently, we parameterized ab initio calculations on mercury-water clusters to describe the mercury-water potential. The liquid mercury phase is approximated
Thermal conductivity of ZnTe investigated by molecular dynamics
Hanfu Wang; Weiguo Chu
2009-01-01
The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green–Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800K. The calculated thermal conductivities are in agreement with the experimental values between 150K and 300K,
Sanville, Edward J [Los Alamos National Laboratory; Bock, Nicolas [Los Alamos National Laboratory; Challacombe, William M [Los Alamos National Laboratory; Cawkwell, Marc J [Los Alamos National Laboratory; Niklasson, Anders M N [Los Alamos National Laboratory; Dattelbaum, Dana M [Los Alamos National Laboratory; Sheffield, Stephen [Los Alamos National Laboratory; Sewell, Thomas D [UNIV OF MISSOURI
2010-01-01
A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.
Combined molecular dynamics-spin dynamics simulations of bcc iron
Perera, Meewanage Dilina N [ORNL] [ORNL; Yin, Junqi [ORNL] [ORNL; Landau, David P [University of Georgia, Athens, GA] [University of Georgia, Athens, GA; Nicholson, Don M [ORNL] [ORNL; Stocks, George Malcolm [ORNL] [ORNL; Eisenbach, Markus [ORNL] [ORNL; Brown, Greg [ORNL] [ORNL
2014-01-01
Using a classical model that treats translational and spin degrees of freedom on an equal footing, we study phonon-magnon interactions in BCC iron with combined molecular and spin dynamics methods. The atomic interactions are modeled via an empirical many-body potential while spin dependent interactions are established through a Hamiltonian of the Heisenberg form with a distance dependent magnetic exchange interaction obtained from first principles electronic structure calculations. The temporal evolution of translational and spin degrees of freedom was determined by numerically solving the coupled equations of motion, using an algorithm based on the second order Suzuki-Trotter decomposition of the exponential operators. By calculating Fourier transforms of space- and time-displaced correlation functions, we demonstrate that the the presence of lattice vibrations leads to noticeable softening and damping of spin wave modes. As a result of the interplay between lattice and spin subsystems, we also observe additional longitudinal spin wave excitations, with frequencies which coincide with that of the longitudinal lattice vibrations.
Iyengar, Srinivasan S.
Quantum Wavepacket Ab Initio Molecular Dynamics: An Approach for Computing Dynamically Averaged quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum
Preserving the Boltzmann ensemble in replica-exchange molecular dynamics
Ben Cooke; Scott C. Schmidler
2008-01-01
We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible,
Computer Simulations of Protein Folding by Targeted Molecular Dynamics
Caflisch, Amedeo
Computer Simulations of Protein Folding by Targeted Molecular Dynamics Philippe Ferrara, Joannis ABSTRACT We have performed 128 folding and 45 unfolding molecular dynamics runs of chymotryp- sin inhibitor;39:252260. © 2000 Wiley-Liss, Inc. Key words: protein folding; chymotrypsin inhibitor 2; molecular dynamics
Molecular dynamics simulations of protein folding from the transition state
Caflisch, Amedeo
Molecular dynamics simulations of protein folding from the transition state Jo¨ 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
Polar solvation dynamics of lysozyme from molecular dynamics studies
NASA Astrophysics Data System (ADS)
Sinha, Sudipta Kumar; Bandyopadhyay, Sanjoy
2012-05-01
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.
Molecular profiling of gliomas: potential therapeutic implications.
Alentorn, Agusti; Duran-Peña, Alberto; Pingle, Sandeep C; Piccioni, David E; Idbaih, Ahmed; Kesari, Santosh
2015-08-01
Gliomas are the most common primary malignant brain tumor. Over the last decade, significant advances have been made in the molecular characterization of this tumor group, identifying predictive biomarkers or molecular actionable targets, and paving the way to molecular-based targeted therapies. This personalized therapeutic approach is effective and illustrated in the present review. Among many molecular abnormalities, BRAF mutation and mTOR activation in pilocytic astrocytomas and subependymal giant cell astrocytomas are actionable targets sensitive to vemurafenib and everolimus, respectively. Chromosome arms 1p/19q co-deletion and IDH mutational status are pivotal in driving delivery of early procarbazine, lomustine and vincristine chemotherapy in anaplastic oligodendroglial tumors. Although consensus to assess MGMT promoter methylation is not reached yet, it may be useful in predicting resistance to temozolomide in elderly patients. PMID:26118895
Molecular Dynamics Simulations of Laser Powered Carbon Nanotube Gears
NASA Technical Reports Server (NTRS)
Srivastava, Deepak; Globus, Al; Han, Jie; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
Dynamics of laser powered carbon nanotube gears is investigated by molecular dynamics simulations with Brenner's hydrocarbon potential. We find that when the frequency of the laser electric field is much less than the intrinsic frequency of the carbon nanotube, the tube exhibits an oscillatory pendulam behavior. However, a unidirectional rotation of the gear with oscillating frequency is observed under conditions of resonance between the laser field and intrinsic gear frequencies. The operating conditions for stable rotations of the nanotube gears, powered by laser electric fields are explored, in these simulations.
NASA Astrophysics Data System (ADS)
Capar, M. Ilk; Nar, A.; Ferrarini, A.; Frezza, E.; Greco, C.; Zakharov, A. V.; Vakulenko, A. A.
2013-03-01
The connection between the molecular structure of liquid crystals and their elastic properties, which control the director deformations relevant for electro-optic applications, remains a challenging objective for theories and computations. Here, we compare two methods that have been proposed to this purpose, both characterized by a detailed molecular level description. One is an integrated molecular dynamics-statistical mechanical approach, where the bulk elastic constants of nematics are calculated from the direct correlation function (DCFs) and the single molecule orientational distribution function [D. A. McQuarrie, Statistical Mechanics (Harper & Row, New York, 1973)]. The latter is obtained from atomistic molecular dynamics trajectories, together with the radial distribution function, from which the DCF is then determined by solving the Ornstein-Zernike equation. The other approach is based on a molecular field theory, where the potential of mean torque experienced by a mesogen in the liquid crystal phase is parameterized according to its molecular surface. In this case, the calculation of elastic constants is combined with the Monte Carlo sampling of single molecule conformations. Using these different approaches, but the same description, at the level of molecular geometry and torsional potentials, we have investigated the elastic properties of the nematic phase of two typical mesogens, 4'-n-pentyloxy-4-cyanobiphenyl and 4'-n-heptyloxy-4-cyanobiphenyl. Both methods yield K3(bend) >K1 (splay) >K2 (twist), although there are some discrepancies in the average elastic constants and in their anisotropy. These are interpreted in terms of the different approximations and the different ways of accounting for the structural properties of molecules in the two approaches. In general, the results point to the role of the molecular shape, which is modulated by the conformational freedom and cannot be fully accounted for by a single descriptor such as the aspect ratio.
Cortes-Huerto, R.
The effect of temperature on the formation and growth of monoatomic chains is investigated by extensive molecular dynamics simulations using a semiempirical potential based on the second-moment approximation to the ...
Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations
Cai, Wei
Plasticity of metal wires in torsion: molecular dynamics and dislocation dynamics simulations-4040 Abstract The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics metal wires controls the mechanisms of plastic deformation. For wires oriented along 110 , dislocations
ATTAINING POTENTIALLY GOOD REDUCTION IN ARITHMETIC DYNAMICS
Benedetto, Rob
ATTAINING POTENTIALLY GOOD REDUCTION IN ARITHMETIC DYNAMICS ROBERT L. BENEDETTO Abstract. Let K be a non-archimedean field, and let K(z) be a rational function of degree d 2. If has potentially good/K such that is conjugate over L to a map of good reduction. In particular, if d = 2 or d is less than the residue
Molecular dynamics simulation of layered double hydroxides
KALINICHEV,ANDREY G.; WANG,JIANWEI; KIRKPATRICK,R. JAMES; CYGAN,RANDALL T.
2000-05-19
The interlayer structure and the dynamics of Cl{sup {minus}} ions and H{sub 2}O molecules in the interlayer space of two typical LDH [Layered Double Hydroxide] phases were investigated by molecular dynamics computer simulations. The simulations of hydrocalumite, [Ca{sub 2}Al(OH){sub 6}]Cl{center_dot}2H{sub 2}O reveal significant dynamic disorder in the orientations of interlayer water molecules. The hydration energy of hydrotalcite, [Mg{sub 2}Al(0H){sub 6}]Cl{center_dot}nH{sub 2}O, is found to have a minimum at approximately n = 2, in good agreement with experiment. The calculated diffusion coefficient of Cl{sup {minus}} as an outer-sphere surface complex is almost three times that of inner-sphere Cl{sup {minus}}, but is still about an order of magnitude less than that of Cl{sup {minus}} in bulk solution. The simulations demonstrate unique capabilities of combined NMR and molecular dynamics studies to understand the structure and dynamics of surface and interlayer species in mineral/water systems.
Molecular Dynamics Simulations of Alpha-synuclein
NASA Astrophysics Data System (ADS)
Sammalkorpi, Maria; Schreck, Carl; Nath, Abhinav; Dewitt, David; Rhoades, Elizabeth; O'Hern, Corey
2011-03-01
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.
Molecular dynamics of a model dimerizing fluid.
Bertrand, C E; Liu, Y
2015-01-28
A model dimer forming fluid has been investigated by continuous molecular dynamics simulations. This study emphasizes the volume fraction and temperature dependence of the dynamic properties of the system, including the self and collective diffusion coefficients and the forward and reverse rate constants. The self and collective diffusion coefficients are found to be well described by a monomer fraction controlled interpolation formula. The forward rate constant (dimer formation) is found to be weakly temperature dependent and strongly volume fraction dependent. The opposite holds for the reverse rate constant. The dimer and monomer decay rates are not found to affect the intermediate scattering functions at the conditions studied. PMID:25637991
Molecular dynamics studies of polyurethane nanocomposite hydrogels
NASA Astrophysics Data System (ADS)
Strankowska, J.; Piszczyk, ?.; Strankowski, M.; Danowska, M.; Szutkowski, K.; Jurga, S.; Kwela, J.
2013-10-01
Polyurethane PEO-based hydrogels have a broad range of biomedical applicability. They are attractive for drug-controlled delivery systems, surgical implants and wound healing dressings. In this study, a PEO based polyurethane hydrogels containing Cloisite® 30B, an organically modified clay mineral, was synthesized. Structure of nanocomposite hydrogels was determined using XRD technique. Its molecular dynamics was studied by means of NMR spectroscopy, DMA and DSC analysis. The mechanical properties and thermal stability of the systems were improved by incorporation of clay and controlled by varying the clay content in polymeric matrix. Molecular dynamics of polymer chains depends on interaction of Cloisite® 30B nanoparticles with soft segments of polyurethanes. The characteristic nanosize effect is observed.
Piero Procacci; Tom A. Darden; Emanuele Paci; Massimo Marchi
1997-01-01
In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines . state-of-the-art molecular dynamics MD algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a
New faster CHARMM molecular dynamics engine.
Hynninen, Antti-Pekka; Crowley, Michael F
2014-02-15
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
Banerjee, Anupam G; Das, Nirupam; Shengule, Sushant A; Srivastava, Radhey Shyam; Shrivastava, Sushant Kumar
2015-08-28
A series of triazin-3(2H)-one derivatives bearing 1,3,4-oxadiazole (4a-4o) were synthesized, characterized and evaluated for anti-inflammatory and analgesic activities. Preliminary in vitro anti-inflammatory activity was assessed using an albumin denaturation assay. The promising compounds were further evaluated in acute, sub-chronic and chronic animal models of inflammation. Derivatives 4d, 4e, 4g, 4j and 4l exhibited significant anti-inflammatory activity with reduced ulcerogenic, hepatotoxic and renotoxic liabilities compared to standard indomethacin. These potential derivatives were also evaluated for in vivo analgesic activity using a writhing model and the formalin-induced paw licking response in mice. Compounds 4d, 4e and 4g exhibited comparable analgesic activity, whereas 4j and 4l yielded moderate effects. The specificity of compounds 4d, 4e, 4g, 4j, and 4l to inhibit (cyclooxygenase-1) COX-1 and (cyclooxygenase-2) COX-2 isozymes and their kinetics were also determined via an in vitro COX inhibition assay. In silico docking studies were performed using a molecular dynamics simulation of the most active compound 4d (COX-2 IC50: 3.07 ?M) at the COX-2 active site. The outcome of this exercise helped to verify the consensual interaction of these compounds with the enzyme. PMID:26117820
Control-volume representation of molecular dynamics
E. R. Smith; D. M. Heyes; D. Dini; T. A. Zaki
2012-05-24
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.
Learning generative models of molecular dynamics
2012-01-01
We introduce three algorithms for learning generative models of molecular structures from molecular dynamics simulations. The first algorithm learns a Bayesian-optimal undirected probabilistic model over user-specified covariates (e.g., fluctuations, distances, angles, etc). L1 reg-ularization is used to ensure sparse models and thus reduce the risk of over-fitting the data. The topology of the resulting model reveals important couplings between different parts of the protein, thus aiding in the analysis of molecular motions. The generative nature of the model makes it well-suited to making predictions about the global effects of local structural changes (e.g., the binding of an allosteric regulator). Additionally, the model can be used to sample new conformations. The second algorithm learns a time-varying graphical model where the topology and parameters change smoothly along the trajectory, revealing the conformational sub-states. The last algorithm learns a Markov Chain over undirected graphical models which can be used to study and simulate kinetics. We demonstrate our algorithms on multiple molecular dynamics trajectories. PMID:22369071
Control-volume representation of molecular dynamics
NASA Astrophysics Data System (ADS)
Smith, E. R.; Heyes, D. M.; Dini, D.; Zaki, T. A.
2012-05-01
A molecular dynamics (MD) parallel to the control volume (CV) formulation of fluid mechanics is developed by integrating the formulas of Irving and Kirkwood [J. Chem. Phys.JCPSA60021-960610.1063/1.1747782 18, 817 (1950)] over a finite cubic volume of molecular dimensions. The Lagrangian molecular system is expressed in terms of an Eulerian CV, which yields an equivalent to Reynolds’ transport theorem for the discrete system. This approach casts the dynamics of the molecular system into a form that can be readily compared to the continuum equations. The MD equations of motion are reinterpreted in terms of a Lagrangian-to-control-volume (LCV) conversion function ?i for each molecule i. The LCV function and its spatial derivatives are used to express fluxes and relevant forces across the control surfaces. The relationship between the local pressures computed using the volume average [Lutsko, J. Appl. Phys.JAPIAU0021-897910.1063/1.341877 64, 1152 (1988)] techniques and the method of planes [Todd , Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.52.1627 52, 1627 (1995)] emerges naturally from the treatment. Numerical experiments using the MD CV method are reported for equilibrium and nonequilibrium (start-up Couette flow) model liquids, which demonstrate the advantages of the formulation. The CV formulation of the MD is shown to be exactly conservative and is, therefore, ideally suited to obtain macroscopic properties from a discrete system.
Particle dynamics in a virtual harmonic potential
NASA Astrophysics Data System (ADS)
Gavrilov, Mom?ilo; Jun, Yonggun; Bechhoefer, John
2013-09-01
Feedback traps can create arbitrary virtual potentials for exploring the dynamics of small Brownian particles. In a feedback trap, the particle position is measured periodically and, after each measurement, one applies the force that would be produced by the gradient of the "virtual potential," at the particle location. Virtual potentials differ from real ones in that the feedback loop introduces dynamical effects not present in ordinary potentials. These dynamical effects are caused by small time scales associated with the feedback, including the delay between the measurement of a particle's position and the feedback response, the feedback response that is applied for a finite update time, and the finite camera exposure from integrating motion. Here, we characterize the relevant experimental parameters and compare to theory the observed power spectra and variance for a particle in a virtual harmonic potential. We show that deviations from the dynamics expected of a continuous potential are measured by the ratio of these small time scales to the relaxation time scale of the virtual potential.
Dynamical nucleus-nucleus potential and incompressibility of nuclear matter
V. Zanganeh; N. Wang; O. N. Ghodsi
2012-03-01
The dynamical nucleus-nucleus potentials for some fusion reactions are investigated by using the improved quantum molecular dynamics (ImQMD) model with different sets of parameters in which the corresponding incompressibility coefficient of nuclear matter is different. Two new sets of parameters SKP* and IQ3 for the ImQMD model are proposed with the incompressibility coefficient of 195 and 225 MeV, respectively. The measured fusion excitation function for 16O+208Pb and the charge distribution of fragments for Ca+Ca and Au+Au in multi-fragmentation process can be reasonably well reproduced. Simultaneously, the influence of the nuclear matter incompressibility and the range of nucleon-nucleon interaction on the nucleus-nucleus dynamic potential is investigated.
The 2011 Dynamics of Molecular Collisions Conference
Nesbitt, David J. [JILA, NIST
2011-07-11
The Dynamics of Molecular Collisions Conference focuses on all aspects of molecular collisions--experimental & theoretical studies of elastic, inelastic, & reactive encounters involving atoms, molecules, ions, clusters, & surfaces--as well as half collisions--photodissociation, photo-induced reaction, & photodesorption. The scientific program for the meeting in 2011 included exciting advances in both the core & multidisciplinary forefronts of the study of molecular collision processes. Following the format of the 2009 meeting, we also invited sessions in special topics that involve interfacial dynamics, novel emerging spectroscopies, chemical dynamics in atmospheric, combustion & interstellar environments, as well as a session devoted to theoretical & experimental advances in ultracold molecular samples. Researchers working inside & outside the traditional core topics of the meeting are encouraged to join the conference. We invite contributions of work that seeks understanding of how inter & intra-molecular forces determine the dynamics of the phenomena under study. In addition to invited oral sessions & contributed poster sessions, the scientific program included a formal session consisting of five contributed talks selected from the submitted poster abstracts. The DMC has distinguished itself by having the Herschbach Medal Symposium as part of the meeting format. This tradition of the Herschbach Medal was first started in the 2007 meeting chaired by David Chandler, based on a generous donation of funds & artwork design by Professor Dudley Herschbach himself. There are two such awards made, one for experimental & one for theoretical contributions to the field of Molecular Collision Dynamics, broadly defined. The symposium is always held on the last night of the meeting & has the awardees are asked to deliver an invited lecture on their work. The 2011 Herschbach Medal was dedicated to the contributions of two long standing leaders in Chemical Physics, Professor Yuan T. Lee & Professor George Schatz. Professor Lee’s research has been based on the development & use of advanced chemical kinetics & molecular beams to investigate & manipulate the behavior of fundamental chemical reactions. Lee’s work has been recognized by many awards, including the Nobel Prize for Chemistry in 1986, as well as Sloan Fellow, Dreyfus Scholar, Fellowship in the American Academy of Arts & Sciences, Fellowship in the American Physical Society, Guggenheim Fellow, Member National Academy of Sciences, Member Academia Sinica, E.O. Lawrence Award, Miller Professor, Berkeley, Fairchild Distinguished Scholar, Harrison Howe Award, Peter Debye Award, & the National Medal of Science. Lee also has served as the President of the Academia Sinica in Taiwan (ROC). Professor Schatz’s research group is interested in using theory & computation to describe physical phenomena in a broad range of applications relevant to chemistry, physics, biology & engineering. Among the types of applications that we interested are: optical properties of nanoparticles & nanoparticle assemblies; using theory to model polymer properties; DNA structure, thermodynamics & dynamics; modeling self assembly & nanopatterning; & gas phase reaction dynamics. Among his many awards & distinctions have been appointment as an Alfred P. Sloan Research Fellow, Camille & Henry Dreyfus Teacher-Scholar, the Fresenius Award, Fellow of the American Physical Society, the Max Planck Research Award, Fellowship in the American Association for the Advancement of Science, & election to the International Academy of Quantum Molecular Sciences & the American Academy of Arts & Sciences. Dr Schatz is also lauded for his highly successful work as Editor for the Journal of Physical Chemistry. We requested $10,000 from DOE in support of this meeting. The money was distributed widely among the student & post doctoral fellows & some used to attract the very best scientists in the field. The organizers were committed to encouraging women & minorities as well as encourage the field of Chemical Physics in scientific
Bohr Sommerfeld quantisation and molecular potentials
Shayak Bhattacharjee; D. S. Ray; J. K. Bhattacharjee
2011-12-19
We use the Bohr Sommerfeld quantization rule along with a perturbative evaluation of the action intergral to find exact energy levels for the P\\"oschl-Teller potential (both hyperbolic and trigonometric forms), the Morse potential, and the Rosen Morse potential. Combining perturbation theory with the simplest asymptotic evaluation of the action integral allows us to obtain all the energy levels of the Lennard-Jones potential with an accuracy greater than 0.1 per cent and serves to confirm that the perturbation results for P\\"oschl-Teller and Morse Potentials are exact.
Ungar, L W; Scherer, N F; Voth, G A
1997-01-01
Classical molecular dynamics simulations are used to investigate the nuclear motions associated with photoinduced electron transfer in plastocyanin. The blue copper protein is modeled using a molecular mechanics potential; potential parameters for the copper-protein interactions are determined using an x-ray crystallographic structure and absorption and resonance Raman spectra. Molecular dynamics simulations yield a variety of information about the ground (oxidized) and optically excited (charge-transfer) states: 1) The probability distribution of the potential difference between the states, which is used to determine the coordinate and energy displacements, places the states well within the Marcus inverted region. 2) The two-time autocorrelation function of the difference potential in the ground state and the average of the difference potential after instantaneous excitation to the excited state are very similar (confirming linear response in this system); their decay indicates that vibrational relaxation occurs in about 1 ps in both states. 3) The spectral densities of various internal coordinates begin to identify the vibrations that affect the optical transition; the spectral density of the difference potential correlation function should also prove useful in quantum simulations of the back electron transfer. 4) Correlation functions of the protein atomic motions with the difference potential show that the nuclear motions are correlated over a distance of more than 20 A, especially along proposed electron transport paths. Images FIGURE 1 FIGURE 7 PMID:8994588
(Molecular understanding of mutagenicity using potential energy methods)
Broyde, S.
1990-01-01
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.
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
Roie Volkovich; Uri Peskin
2010-12-01
The possibility of using single molecule junctions as electron pumps for energy conversion and storage is considered. It is argued that the small dimensions of these systems enable to make use of unique intra-molecular quantum coherences in order to pump electrons between two leads and to overcome relaxation processes which tend to suppress the pumping efficiency. In particular, we demonstrate that a selective transient excitation of one chromophore in a bi-chromophoric donor-bridge-acceptor molecular junction model yields currents which transfer charge (electron and holes) unevenly to the two leads in the absence of a bias potential. The utility of this mechanism for charge pumping in steady state conditions is proposed.
Molecular interferometer to decode attosecond electron-nuclear dynamics
NASA Astrophysics Data System (ADS)
Palacios, Alicia; González-Castrillo, Alberto; Martin, Fernando
2015-05-01
A full characterization of the coupled electronic and nuclear dynamics in molecules is achieved by using an attosecond XUV-pump/XUV-probe scheme. The complete information on the wave packet generated by the pump pulse is obtained without introducing significant distortions through the pulses themselves. Theoretical ab initio calculations are presented for the hydrogen molecule, together with simple models for interpretation that can be easily extrapolated to larger systems. Different from the commonly used XUV-IR schemes, where the observed dynamics is typically dominated by the relatively strong IR field, XUV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In the work presented here, the molecule is illuminated with twin XUV pulses with a given delay, creating a molecular interferometer due to electron ejection through both direct and sequential two-photon absorption leaving the molecule in the same final vibronic state.
Molecular dynamics equation of state for nonpolar geochemical fluids
NASA Astrophysics Data System (ADS)
Duan, Zhenhao; Møller, Nancy; Wears, John H.
1995-04-01
Remarkable agreement between molecular dynamics simulations and experimental measurements has been obtained for methane for a large range of intensive variables, including those corresponding to liquid/vapor coexistence. Using a simple Lennard-Jones potential the simulations not only predict the PVT properties up to 2000°C and 20,000 bar with errors less than 1.5%, but also reproduce phase equilibria well below 0°C with accuracy close to experiment. This two-parameter molecular dynamics equation of state (SOS) is accurate for a much larger range of temperatures and pressures than our previously published EOS with a total fifteen parameters or that of Angus et al. (1978) with thirty-three parameters. By simple scaling, it is possible to predict PVT and phase equilibria of other nonpolar and weakly polar species.
Supercritical ammonia: a molecular dynamics simulation and vibrational spectroscopic investigation.
Tassaing, T; Soetens, J-C; Vyalov, I; Kiselev, M; Idrissi, A
2010-12-01
Combining infrared spectroscopy and molecular dynamics simulations, we have investigated the structural and dynamical properties of ammonia from liquid state (T = 220 and 303 K) up to the supercritical domain along the isotherm T = 423 K. Infrared spectra show that the N-H stretching and bending modes are significantly perturbed which is interpreted as a signature of the change of the local environment. In order to compare the experimental spectra with those obtained using molecular dynamics simulation, we have used a flexible four sites model which allows to take into account the anharmonicity in all the vibration modes particularly that of the inversion mode of the molecule. A good agreement between our experimental and calculated spectra has been obtained hence validating the intermolecular potential used in this study to simulate supercritical ammonia. The detailed analysis of the molecular dynamics simulation results provides a quantitative insight of the relative importance of hydrogen bonding versus nonhydrogen bonded interactions that governs the structure of fluid ammonia. PMID:21142306
Thermal conductivity of molecular chains with asymmetric potentials of pair interactions.
Savin, Alexander V; Kosevich, Yuriy A
2014-03-01
We provide molecular-dynamics simulation of heat transport in one-dimensional molecular chains with different interparticle pair potentials. We show that the thermal conductivity is finite in the thermodynamic limit in chains with the potentials that allow for bond dissociation. The Lennard-Jones, Morse, and Coulomb potentials are such potentials. The convergence of the thermal conductivity is provided by phonon scattering on the locally strongly stretched loose interatomic bonds at low temperature and by the many-particle scattering at high temperature. On the other hand, chains with a confining pair potential, which does not allow for bond dissociation, possess anomalous thermal conductivity, diverging with the chain length. We emphasize that chains with a symmetric or asymmetric Fermi-Pasta-Ulam potential or with combined potentials, containing a parabolic and/or a quartic confining potential, all exhibit anomalous heat transport. PMID:24730785
Photomechanical spallation of molecular and metal targets: molecular dynamics study
NASA Astrophysics Data System (ADS)
Leveugle, E.; Ivanov, D. S.; Zhigilei, L. V.
Microscopic mechanisms of photomechanical spallation are investigated in a series of large-scale molecular dynamics simulations performed for molecular and metal targets. A mesoscopic breathing sphere model is used in simulations of laser interaction with molecular targets. A coupled atomistic-continuum model that combines a molecular dynamics method with a continuum description of the laser excitation and subsequent relaxation of the conduction band electrons is used for metal targets. Similar mechanisms of the laser-induced photomechanical spallation are observed for molecular and metal targets. For both target materials, the relaxation of compressive stresses generated under conditions of stress confinement is found to be the main driving force for the nucleation, growth and coalescence of voids in a subsurface region of an irradiated target at laser fluences close to the threshold for fragmentation. The mechanical stability of the region subjected to the void nucleation is strongly affected by the laser heating and the depth of the spallation region in bulk targets is much closer to the surface as compared with the depth where the maximum tensile stresses are generated. Two stages can be identified in the evolution of voids in laser spallation, the initial void nucleation and growth, with the number of voids of all sizes increasing, followed by void coarsening and coalescence, when the number of large voids increases at the expense of the quickly decreasing population of small voids. The void volume distributions are found to be relatively well described by the power law N(V) V-?, with exponent gradually increasing with time. Comparison of the simulation results obtained for Ni films of two different thicknesses and bulk Ni targets suggests that the size/shape of the target plays an important role in laser spallation. The reflection of the laser-induced pressure wave from the back surface of a film results in higher maximum tensile stresses and lower threshold fluence for spallation. As the size of the film increases, the locations of the spallation region and the region of the maximum tensile stresses are splitting apart and the threshold fluence for spallation increases.
On the ionization potential of molecular oxygen
NASA Technical Reports Server (NTRS)
Samson, J. A. R.; Gardner, J. L.
1974-01-01
The ionization potential of O2 was measured by the technique of high resolution photoelectron spectroscopy taking into account the influence of rotational structure on the shape of the vibrational bands. A value of 12.071 + or - .001 eV (1027.1 + or - 0.1 A) was found for the ionization potential. A lowering of the ionization potential caused by a branch-head when delta N = -2 gave an appearance potential for ionization of 12.068 + or - .001 eV (1027.4 + or - 0.1 A).
On the dynamics of molecular conformation
Mezi?, Igor
2006-01-01
Understanding the mechanism of fast transitions between conformed states of large biomolecules is central to reconciling the dichotomy between the relatively high speed of metabolic processes and slow (random-walk based) estimates on the speed of biomolecular processes. Here we use the dynamical systems approach to suggest that the reduced time of transition between different conformations is due to features of the dynamics of molecules that are a consequence of their structural features. Long-range and local effects both play a role. Long-range molecular forces account for the robustness of final states and nonlinear processes that channel localized, bounded disturbances into collective, modal motions. Local interconnections provide fast transition dynamics. These properties are shared by a class of networked systems with strong local interconnections and long-range nonlinear forces that thus exhibit flexibility and robustness at the same time. PMID:16675553
Molecular dynamics simulations of magnetized dusty plasmas
NASA Astrophysics Data System (ADS)
Piel, Alexander; Reichstein, Torben; Wilms, Jochen
2012-10-01
The combination of the electric field that confines a dust cloud with a static magnetic field generally leads to a rotation of the dust cloud. In weak magnetic fields, the Hall component of the ion flow exerts a drag force that sets the dust in rotation. We have performed detailed molecular-dynamics simulations of the dynamics of torus-shaped dust clouds in anodic plasmas. The stationary flow [1] is characterized by a shell structure in the laminar dust flow and by the spontaneous formation of a shear-flow around a stationary vortex. Here we present new results on dynamic phenomena, among them fluctuations due to a Kelvin-Helmholtz instability in the shear-flow. The simulations are compared with experimental results. [4pt] [1] T. Reichstein, A. Piel, Phys. Plasmas 18, 083705 (2011)
Electron and molecular dynamics: Penning ionization and molecular charge transport
NASA Astrophysics Data System (ADS)
Madison, Tamika Arlene
An understanding of fundamental reaction dynamics is an important problem in chemistry. In this work, experimental and theoretical methods are combined to study the dynamics of fundamental chemical reactions. Molecular collision and dissociation dynamics are explored with the Penning ionization of amides, while charge transfer reactions are examined with charge transport in organic thin film devices. Mass spectra from the Penning ionization of formamide by He*, Ne*, and Ar* were measured using molecular beam experiments. When compared to 70eV electron ionization spectra, the He* and Ne* spectra show higher yields of fragments resulting from C--N and C--H bond cleavage, while the Ar* spectrum only shows the molecular ion, H-atom elimination, and decarbonylation. The differences in yields and observed fragments are attributed to the differences in the dynamics of the two ionization methods. Fragmentation in the Ar* spectrum was analyzed using quantum chemistry and RRKM calculations. Calculated yields for the Ar* spectrum are in excellent agreement with experiment and show that 15% and 50% of the yields for decarbonylation and H-atom elimination respectively are attributed to tunneling. The effects of defects, traps, and electrostatic interactions on charge transport in imperfect organic field effect transistors were studied using course-grained Monte Carlo simulations with explicit introduction of defect and traps. The simulations show that electrostatic interactions dramatically affect the field and carrier concentration dependence of charge transport in the presence of a significant number of defects. The simulations also show that while charge transport decreases linearly as a function of neutral defect concentration, it is roughly unaffected by charged defect concentration. In addition, the trap concentration dependence on charge transport is shown to be sensitive to the distribution of trap sites. Finally, density functional theory calculations were used to study how charge localization affects the orbital energies of positively charged bithiophene clusters. These calculations show that the charge delocalizes over at least seven molecules, is more likely to localize on "tilted" molecules due to polarization effects, and affects molecules anisotropically. These results suggest that models for charge transport in organic semiconductors should be modified to account for charge delocalization and intermolecular interactions.
Large scale molecular dynamics simulations of nuclear pasta
NASA Astrophysics Data System (ADS)
Horowitz, C. J.; Berry, D.; Briggs, C.; Chapman, M.; Clark, E.; Schneider, A.
2014-09-01
We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. We report large-scale molecular dynamics simulations of nuclear pasta using from 50,000 to more than 3,000,000 nucleons. We use a simple phenomenological two-nucleon potential that reproduces nuclear saturation. We find a complex ``nuclear waffle'' phase in addition to more conventional rod, plate, and sphere phases. We also find long-lived topological defects involving screw like dislocations that may reduce the electrical conductivity and thermal conductivity of lasagna phases. From MD trajectories we calculate a variety of quantities including static structure factor, dynamical response function, shear modulus and breaking strain. Supported in parts by DOE Grants No. DE-FG02-87ER40365 (Indiana University) and No. DE-SC0008808 (NUCLEI SciDAC Collaboration).
Thermal Transport in Carbon Nanotubes using Molecular Dynamics
NASA Astrophysics Data System (ADS)
Moore, Andrew; Khatun, Mahfuza
2011-10-01
We will present results of thermal transport phenomena in Carbon Nanotube (CNT) structures. CNTs have many interesting physical properties, and have the potential for device applications. Specifically, CNTs are robust materials with high thermal conductance and excellent electrical conduction properties. A review of electrical and thermal conduction of the structures will be discussed. The research requires analytical analysis as well as simulation. The major thrust of this study is the usage of the molecular dynamics (MD) simulator, LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). A significant investigation using the LAMMPS code is conducted on the existing Beowulf Computing Cluster at BSU. NanoHUB, an open online resource to the entire nanotechnology community developed by the researchers of Purdue University, is used for further supplementary resources. Results will include the time-dependence of temperature, kinetic energy, potential energy, heat flux correlation, and heat conduction.
Molecular-dynamics simulations of void collapse in shocked model-molecular solids
NASA Astrophysics Data System (ADS)
Mintmire, J. W.; Robertson, D. H.; White, C. T.
1994-06-01
We have carried out a series of molecular-dynamics simulations on a model three-dimensional molecular solid to study the dynamics of shock-induced collapse of void defects. Molecular-dynamics methods were used for a model system of identical particles arranged as diatomic molecules aligned with the center of mass of each molecule at fcc lattice sites, using a \\{111\\} layering for the two-dimensional boundary conditions. The diatoms were internally coupled via a harmonic potential; all other interactions were modeled with Morse potentials between all particles other than the immediate diatomic partner. Using this model, we have investigated the effect of a cylindrical void at right angles to the direction of layering (and impact). Depending on the strength of the incident shock wave, the void is found to collapse either smoothly and symmetrically (like a balloon gradually losing air), or asymmetrically and turbulently. In the latter case, we note the transient formation (for periods of several hundreds of femtoseconds) of ``hot spots'' at the void location both in terms of the local effective temperature and the vibrational energies of the diatoms.
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 ...
Tunable Interfacial Thermal Conductance by Molecular Dynamics
NASA Astrophysics Data System (ADS)
Shen, Meng
We study the mechanism of tunable heat transfer through interfaces between solids using a combination of non-equilibrium molecular dynamics simulation (NEMD), vibrational mode analysis and wave packet simulation. We investigate how heat transfer through interfaces is affected by factors including pressure, interfacial modulus, contact area and interfacial layer thickness, with an overreaching goal of developing fundamental knowledge that will allow one to tailor thermal properties of interfacial materials. The role of pressure and interfacial stiffness is unraveled by our studies on an epitaxial interface between two Lennard-Jones (LJ) crystals. The interfacial stiffness is varied by two different methods: (i) indirectly by applying pressure which due to anharmonic nature of bonding, increases interfacial stiffness, and (ii) directly by changing the interfacial bonding strength by varying the depth of the potential well of the LJ potential. When the interfacial bonding strength is low, quantitatively similar behavior to pressure tuning is observed when the interfacial thermal conductance is increased by directly varying the potential-well depth parameter of the LJ potential. By contrast, when the interfacial bonding strength is high, thermal conductance is almost pressure independent, and even slightly decreases with increasing pressure. This decrease can be explained by the change in overlap between the vibrational densities of states of the two crystalline materials. The role of contact area is studied by modeling structures comprised of Van der Waals junctions between single-walled nanotubes (SWCNT). Interfacial thermal conductance between SWCNTs is obtained from NEMD simulation as a function of crossing angle. In this case the junction conductance per unit area is essentially a constant. By contrast, interfacial thermal conductance between multiwalled carbon nanotubes (MWCNTs) is shown to increase with diameter of the nanotubes by recent experimental studies [1]. To elucidate this behavior we studied a simplified model comprised of an interface between two stacks of graphene ribbons to mimic the contact between multiwalled nanotubes. Our results, in agreement with experiment, show that the interfacial thermal conductance indeed increases with the number of graphene layers, corresponding to larger diameter and larger number of walls in MWCNT. The role of interfacial layer thickness is investigated by modeling a system of a few layers of graphene sandwiched between two silicon slabs. We show, by wave packet simulation and by theoretical calculation of a spring-mass model, that the transmission coefficient of individual vibrational modes is strongly dependent on the frequency and the number of graphene layers due to coherent interference effects; by contrast, the interfacial thermal conductance obtained in NEMD simulation, which represents an integral over all phonons, is essentially independent of the number of graphene layers, in agreement with recent experiments. Furthermore, when we heat one atomic layer of graphene directly, the effective interfacial conductance associated with heat dissipation to the silicon substrate is very small. We attribute this to the resistance associated with heat transfer between high and low frequency phonon modes within graphene. Finally, we also replaced graphene layers by a few WSe2 sheets and observed that interfacial thermal resistance of a Si/n-WSe2/Si structure increases linearly with interface thickness at least for 1 < n <= 20, indicating diffusive heat transfer mechanism, in contrast to ballistic behavior of a few graphene layers. The corresponding thermal conductivity (0.048 W m-1 K-1) of a few WSe2 layers is rather small. By comparing phonon dispersion of graphene layers and WSe2 sheets, we attribute the diffusive behavior of a few WSe2 sheets to abundant optical phonons at low and medium frequencies leading to very short mean free path. Our computational studies of effects of pressure and structural properties on interfacial thermal conductance provide fundamental in
Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics
Zhao, Hongkai
most particles in molecular dynamics are to represent water molecules solvating the target biomolecules1 Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision the boundary force calculation. #12;2 Introduction Biomolecules are highly complex molecular machines
Molecular gas and the dynamics of galaxies
F. Combes
1999-02-01
In this review, I discuss some highlights of recent research on molecular gas in galaxies; large-scale CO maps of nearby galaxies are being made, which extend our knowledge on global properties, radial gradients, and spiral structure of the molecular ISM. Very high resolution are provided by the interferometers, that reveal high velocity gradients in galaxy nuclei, and formation of embedded structures, like bars within bars. Observation of the CO and other lines in starburst galaxies have questioned the H2-to-CO conversion factor. Surveys of dwarfs have shown how the conversion factor depends on metallicity. The molecular content is not deficient in galaxy clusters, as is the atomic gas. Galaxy interactions are very effective to enhance gas concentrations and trigger starbursts. Nuclear disks or rings are frequently observed, that concentrate the star formation activity. Since the density of starbursting galaxies is strongly increasing with redshift, the CO lines are a privileged tool to follow evolution of galaxies and observe the ISM dynamics at high redshift: due to the high excitation of the molecular gas, the stronger high-$J$ CO lines are redshifted into the observable band, which facilitates the detection.
DYNAMICAL ANALYSIS OF HIGHLY EXCITED MOLECULAR SPECTRA
Michael E. Kellman
2005-06-17
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.
Fast method for quantum mechanical molecular dynamics
Niklasson, Anders M N
2012-01-01
With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science, chemistry and biology. Nevertheless, the computational cost still remains prohibitively large in many cases, particularly in comparison to classical MD simulations using empirical force fields. Here we show how to circumvent the major computational bottleneck in Born-Oppenheimer MD simulations arising from the self-consistent-charge optimization. The optimization-free quantum mechanical MD method is demonstrated for density functional tight-binding theory. The molecular trajectories are almost indistinguishable from an "exact" microcanonical Born-Oppenheimer MD simulation even when linear scaling sparse matrix algebra is used. Our findings drastically reduce the computational gap between classical and quantum mechanical MD simulations.
Rotary ATPases--dynamic molecular machines.
Stewart, Alastair G; Laming, Elise M; Sobti, Meghna; Stock, Daniela
2014-04-01
Recent work has provided the detailed overall architecture and subunit composition of three subtypes of rotary ATPases. Composite models of F-type, V-type and A-type ATPases have been constructed by fitting high-resolution X-ray structures of individual components into electron microscopy derived envelopes of the intact enzymes. Electron cryo-tomography has provided new insights into the supra-molecular arrangement of eukaryotic ATP synthases within mitochondria. An inherent flexibility in rotary ATPases observed by different techniques suggests greater dynamics during operation than previously envisioned. The concerted movement of subunits within the complex might provide means of regulation and information transfer between distant parts of rotary ATPases thereby fine tuning these molecular machines to their cellular environment, while optimizing their efficiency. PMID:24878343
Attosecond VUV Coherent Control of Molecular Dynamics
Ranitovic, P; Riviere, P; Palacios, A; Tong, X M; Toshima, N; Gonzalez-Castrillo, A; Martin, L; Martin, F; Murnane, M M; Kapteyn, H C
2014-01-01
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 manipula...
Molecular dynamics simulations of membrane proteins.
Pluhackova, Kristyna; Wassenaar, Tsjerk A; Böckmann, Rainer A
2013-01-01
Molecular dynamics simulations are a powerful tool for complementing experimental studies, providing insights in biological processes at the molecular and atomistic level, at timescales from picoseconds to microseconds. Simulations are useful for testing hypotheses and can provide explanations for experimental observations as well as suggestions for further experiments. This does require that the simulation setup allows assessment of the question addressed. For example, it is evident that for simulation of a protein in its functional state the protein model and the environment have to mimic the biological situation as close as possible. In this chapter, a general strategy is presented for setting up and running simulations of membrane proteins of known structure in biological membranes of diverse composition and size. PMID:23996172
Molecular Dynamics Simulation of Carbon Nanotube Based Gears
NASA Technical Reports Server (NTRS)
Han, Jie; Globus, Al; Jaffe, Richard; Deardorff, Glenn; Chancellor, Marisa K. (Technical Monitor)
1996-01-01
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.
Parameters for molecular dynamics simulations of iron-sulfur proteins.
Carvalho, Alexandra T P; Teixeira, Ana F S; Ramos, Maria J
2013-07-01
Iron-sulfur proteins involved in electron transfer reactions have finely tuned redox potentials, which allow them to be highly efficient and specific. Factors such as metal center solvent exposure, interaction with charged residues, or hydrogen bonds between the ligand residues and amide backbone groups have all been pointed out to cause such specific redox potentials. Here, we derived parameters compatible with the AMBER force field for the metal centers of iron-sulfur proteins and applied them in the molecular dynamics simulations of three iron-sulfur proteins. We used density-functional theory (DFT) calculations and Seminario's method for the parameterization. Parameter validation was obtained by matching structures and normal frequencies at the quantum mechanics and molecular mechanics levels of theory. Having guaranteed a correct representation of the protein coordination spheres, the amide H-bonds and the water exposure to the ligands were analyzed. Our results for the pattern of interactions with the metal centers are consistent to those obtained by nuclear magnetic resonance spectroscopy (NMR) experiments and DFT calculations, allowing the application of molecular dynamics to the study of those proteins. PMID:23609049
Johan Åqvist; Petra Wennerström; Martin Nervall; Sinisa Bjelic; Bjørn O. Brandsdal
2004-01-01
A mixed molecular dynamics\\/Monte Carlo (MD\\/MC) algorithm for constant pressure simulations of arbitrary molecular systems is examined. Calculations are reported at ambient and high pressures both for liquid water systems and for a chemical reaction step in a solvated enzyme utilizing empirical valence bond potentials. The present method reproduces earlier reported results well and is computationally efficient since it does
Implementing peridynamics within a molecular dynamics code.
Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James; Parks, Michael L.
2007-12-01
Peridynamics (PD) is a continuum theory that employs a nonlocal model to describe material properties. In this context, nonlocal means that continuum points separated by a finite distance may exert force upon each other. A meshless method results when PD is discretized with material behavior approximated as a collection of interacting particles. This paper describes how PD can be implemented within a molecular dynamics (MD) framework, and provides details of an efficient implementation. This adds a computational mechanics capability to an MD code, enabling simulations at mesoscopic or even macroscopic length and time scales.
Microscale swimming: The molecular dynamics approach
D. C. Rapaport
2007-12-06
The self-propelled motion of microscopic bodies immersed in a fluid medium is studied using molecular dynamics simulation. The advantage of the atomistic approach is that the detailed level of description allows complete freedom in specifying the swimmer design and its coupling with the surrounding fluid. A series of two-dimensional swimming bodies employing a variety of propulsion mechanisms -- motivated by biological and microrobotic designs -- is investigated, including the use of moving limbs, changing body shapes and fluid jets. The swimming efficiency and the nature of the induced, time-dependent flow fields are found to differ widely among body designs and propulsion mechanisms.
[Oligoglycine surface structures: molecular dynamics simulation].
Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V
2010-01-01
The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements. PMID:21063448
Molecular Dynamics Studies of Graphene Nanobubbles
NASA Astrophysics Data System (ADS)
Qi, Zenan; Park, Harold; Pereira, Vitor M.; Castro-Neto, Antonio H.; Campbell, David K.
2013-03-01
We apply classical molecular dynamics to study pressure-induced deformations and the resulting pseudomagnetic (PSM) fields for monolayer graphene nanobubbles (NBs) of various geometries. We obtain the PSM field distributions for triangular, square, rectangular, hexagonal, and circular graphene NBs and find that in most cases the PSM fields near the tops of the NBs are smaller than around the NB edges. For circular NBs of diameter smaller than about 2nm, we find that the PSM field contribution from bending and curvature becomes comparable to from the traditional in-plane component of the gauge field.
Molecular dynamics simulations of dense plasmas
Collins, L.A.; Kress, J.D.; Kwon, I.; Lynch, D.L.; Troullier, N.
1993-12-31
We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.
Molecular dynamics for ion beam analysis
NASA Astrophysics Data System (ADS)
Nordlund, K.
2008-04-01
Molecular dynamics (MD) computer simulations, while very extensively used in chemistry and materials physics, have largely been absent in the theoretical treatment of ion beam analysis. Instead the computationally more efficient binary collision approximation (BCA) methods are widely used. In this paper I compare the two methods regarding the level of physical approximation versus accuracy, using a simple model study as an illustrative example. I then show, based on results in the literature, that although in most cases BCA methods are well sufficient for ion beam analysis, there are special conditions where MD methods are required even for keV and MeV kinetic energy processes.
Bio-Molecular Dynamics Comes of Age
NSDL National Science Digital Library
Herman J. C. Berendsen (University of Groningen, Netherlands; Department of Biophysical Chemistry and the BIOSON Research Institute)
1996-02-16
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 GrubmÃ¼ller 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.
Mathematical Issues in Molecular Dynamics Robert D. Skeel (Purdue University),
Skeel, Robert
Mathematical Issues in Molecular Dynamics Robert D. Skeel (Purdue University), Paul Tupper (Mc is the probability of two biomolecules being (noncovalently) bound versus unbound. 2. Dynamics. Given the relative is typically unphysical. We begin in Section 2 with a consideration of the models we use in molecular dynamics
Fluid transport properties by equilibrium molecular dynamics. II. Multicomponent systems
Dysthe, Dag Kristian
Fluid transport properties by equilibrium molecular dynamics. II. Multicomponent systems D. K than 25 years molecular dynamics has been used to study fluid transport properties. Such MD studies dynamics has been applied to multicomponent mixtures of flexible, multicenter models of linear and branched
-Value analysis by molecular dynamics simulations of reversible folding
Caflisch, Amedeo
-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 (59) and to bias molecular dynamics (MD) trajectories
Molecular dynamics simulations of nanoindentation and nanotribology.
Kenny, S D; Mulliah, D; Sanz-Navarro, C F; Smith, Roger
2005-08-15
We present results of parallel molecular dynamics simulations of nanoindentation and nanotribology experiments. The models we have developed describe both the sample and the indenter atomistically and model the effect of the cantilevers in an atomic force microscope through the use of springs. We show that the simulations are in good qualitative agreement with experiment and help to elucidate many of the mechanisms that take place during these processes. In particular, we illustrate the role that dislocations play both in nanoindentation and also in stick-slip. Further to this we show how real-time visualization and computational steering have been employed in these simulations to capture the dynamical events that take place. PMID:16099759
A multiscale molecular dynamics allowing macroscale mechanical loads
NASA Astrophysics Data System (ADS)
Tong, Qi; Li, Shaofan
2015-06-01
We proposed a novel multiscale molecular-dynamics model in order to apply macroscale boundary conditions to microscale molecular systems, which is difficult for classical molecular dynamics. Unlike in statistical mechanics, in which macroscale quantities such as temperature and pressure are collected from molecular information, the proposed approach is a reversed procedure to find optimal molecular states when macroscale conditions such as traction are enforced. The model is originated from Parrinello-Rahman molecular dynamics but extends it to solve finite-size, inhomogeneous molecular-dynamics problems by generalizing the representative volume element to a “material point” in continuum mechanics. An example of compressing a nickel nanowire is presented to demonstrate the capacity of the method to simulate localized phase transition in a finite-size molecular system, which validates the effectiveness of the method.
Molecular dynamics of void collapse mechanisms in shocked media
NASA Astrophysics Data System (ADS)
Mintmire, J. W.; Robertson, D. H.; Elert, M. L.; Brenner, D. W.; White, C. T.
1994-07-01
We have carried out a series of molecular dynamics simulations on a model system to study the dynamics of void defect collapse during pressure-wave propagation in condensed-phase systems. Three-dimensional molecular-dynamics methods were used for a model system of identical particles arranged as diatomic molecules aligned with the center of mass of each molecule at fcc lattice sites, using a {111} layering for the two-dimensional boundary conditions. The diatoms were internally coupled via a harmonic potential; all other interactions were modeled with Morse potentials between all particles other than the immediate diatomic partner. Using this model, we have investigated the effect of a cylindrical void at right angles to the direction of layering (and impact). Depending on the energy density of the incident pressure wave, the void defect can either collapse smoothly and symmetrically (as in a balloon gradually losing air), or asymmetrically and turbulently. In the latter case, we note the transient formation (for periods of several hundreds of femtoseconds) of ``hot spots'' at the void location both in terms of the local effective temperature and the vibrational energies of the diatoms.
Laser-induced perturbation into molecular dynamics localized in neuronal cell
NASA Astrophysics Data System (ADS)
Hosokawa, Chie; Takeda, Naoko; Kudoh, Suguru N.; Taguchi, Takahisa
2015-03-01
Molecular dynamics at synaptic terminals in neuronal cells is essential for synaptic plasticity and subsequent modulation of cellular functions in a neuronal network. For realizing artificial control of living neuronal network, we demonstrate laser-induced perturbation into molecular dynamics in the neuronal cells. The optical trapping of cellular molecules such as synaptic vesicles or neural cell adhesion molecules labeled with quantum dots was evaluated by fluorescence imaging and fluorescence correlation spectroscopy. The trapping and assembling dynamics was revealed that the molecular motion was constrained at the focal spot of a focused laser beam due to optical trapping force. Our method has a potential to manipulate synaptic transmission at single synapse level.
The next step in systems biology: simulating the temporospatial dynamics of molecular network.
Zhu, Hao; Huang, Sui; Dhar, Pawan
2004-01-01
As a result of the time- and context-dependency of gene expression, gene regulatory and signaling pathways undergo dynamic changes during development. Creating a model of the dynamics of molecular interaction networks offers enormous potential for understanding how a genome orchestrates the developmental processes of an organism. The dynamic nature of pathway topology calls for new modeling strategies that can capture transient molecular links at the runtime. The aim of this paper is to present a brief and informative, but not all-inclusive, viewpoint on the computational aspects of modeling and simulation of a non-static molecular network. PMID:14696042
ls1 mardyn: The massively parallel molecular dynamics code for large systems
Christoph Niethammer; Stefan Becker; Martin Bernreuther; Martin Buchholz; Wolfgang Eckhardt; Alexander Heinecke; Stephan Werth; Hans-Joachim Bungartz; Colin W. Glass; Hans Hasse; Jadran Vrabec; Martin Horsch
2014-08-20
The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures, and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales which were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multi-center rigid potential models based on Lennard-Jones sites, point charges and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, e.g. for fluids at interfaces, as well as non-equilibrium molecular dynamics simulation of heat and mass transfer.
Frontiers in molecular dynamics simulations of DNA.
Pérez, Alberto; Luque, F Javier; Orozco, Modesto
2012-02-21
It has been known for decades that DNA is extremely flexible and polymorphic, but our knowledge of its accessible conformational space remains limited. Structural data, primarily from X-ray diffraction studies, is sparse in comparison to the manifold configurations possible, and direct experimental examinations of DNA's flexibility still suffer from many limitations. In the face of these shortcomings, molecular dynamics (MD) is now an essential tool in the study of DNA. It affords detailed structural and dynamical insights, which explains its recent transition from a small number of highly specialized laboratories to a large variety of groups dealing with challenging biological problems. MD is now making an irreversible journey to the mainstream of research in biology, with the attendant opportunities and challenges. But given the speed with which MD studies of DNA have spread, the roots remain somewhat shallow: in many cases, there is a lack of deep knowledge about the foundations, strengths, and limits of the technique. In this Account, we discuss how MD has become the most important source of structural and flexibility data on DNA, focusing on advances since 2007 of atomistic MD in the description of DNA under near-physiological conditions and highlighting the possibilities and shortcomings of the technique. The evolution in the field over the past four years is a prelude to the ongoing revolution. The technique has gained in robustness and predictive power, which when coupled with the spectacular improvements in software and hardware has enabled the tackling of systems of increasing complexity. Simulation times of microseconds have now been achieved, with even longer times when specialized hardware is used. As a result, we have seen the first real-time simulation of large conformational transitions, including folding and unfolding of short DNA duplexes. Noteworthy advances have also been made in the study of DNA-ligand interactions, and we predict that a global thermodynamic and kinetic picture of the binding landscape of DNA will become available in a few years. MD will become a crucial tool in areas such as biomolecular engineering and synthetic biology. MD has also been shown to be an excellent source of parameters for mesoscopic models of DNA flexibility. Such models can be refined through atomistic MD simulations on small duplexes and then applied to the study of entire chromosomes. Recent evidence suggests that MD-derived elastic models can successfully predict the position of regulatory regions in DNA and can help advance our understanding of nucleosome positioning and chromatin plasticity. If these results are confirmed, MD simulations can become the ultimate tool to decipher a physical code that can contribute to gene regulation. We are entering the golden age of MD simulations of DNA. Undoubtedly, the expectations are high, but the challenges are also enormous. These include the need for more accurate potential energy functionals and for longer and more complex simulations in more realistic systems. The joint research effort of several groups will be crucial for adapting the technique to the requirements of the coming decade. PMID:21830782
Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite
A. Ito; H. Nakamura
2006-04-26
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.
Statistical Molecular Dynamics study of displacement energies in diamond
NASA Astrophysics Data System (ADS)
Delgado, Diego; Vila, Rafael
2011-12-01
Molecular Dynamics simulations in bulk diamond using AIREBO potential have been used to calculate minimum displacement energy. A statistical approach has been applied calculating displacement probability curves along the main crystallographic directions. With these curves a minimum displacement energy of around 30 eV can be obtained, and a weighted average energy of around 70 eV. This value has been estimated as more accurate for its use in BCA displacement equations to obtain Frenkel pairs at moderate temperatures. This work also includes a study of defect states whose analysis reveals interesting results concerning the evolution of primary damage at higher PKA energies.
Molecular dynamics simulation of crystal growth of undercooled liquid Co
NASA Astrophysics Data System (ADS)
Fang, Teng; Wang, Li; Qi, Yu
2013-08-01
Molecular dynamics simulations have been performed to explore the movement of liquid-solid interface of Co first by using a potential of embedded atom type. By determining the time dependence of the volume per particle for different temperatures, the simulated melting temperature of 1720 K, is in quantitative agreement with the experiment one. The calculated kinetic growth coefficient agrees well with the latest experimental result. The anisotropy of kinetic growth coefficient is given by k100>k110>k111. The activation energy is almost close to zero under high undercoolings, although the crystal growth still proceeds with the speed of about 60 m/s, indicating an athermal process.
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning
NASA Astrophysics Data System (ADS)
Mugnai, Mauro L.; Elber, Ron
2015-01-01
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.
Molecular interferometer to decode attosecond electron–nuclear dynamics
Palacios, Alicia; González-Castrillo, Alberto; Martín, Fernando
2014-01-01
Understanding the coupled electronic and nuclear dynamics in molecules by using pump–probe schemes requires not only the use of short enough laser pulses but also wavelengths and intensities that do not modify the intrinsic behavior of the system. In this respect, extreme UV pulses of few-femtosecond and attosecond durations have been recognized as the ideal tool because their short wavelengths ensure a negligible distortion of the molecular potential. In this work, we propose the use of two twin extreme UV pulses to create a molecular interferometer from direct and sequential two-photon ionization processes that leave the molecule in the same final state. We theoretically demonstrate that such a scheme allows for a complete identification of both electronic and nuclear phases in the wave packet generated by the pump pulse. We also show that although total ionization yields reveal entangled electronic and nuclear dynamics in the bound states, doubly differential yields (differential in both electronic and nuclear energies) exhibit in addition the dynamics of autoionization, i.e., of electron correlation in the ionization continuum. Visualization of such dynamics is possible by varying the time delay between the pump and the probe pulses. PMID:24591647
Exact dynamic properties of molecular motors
NASA Astrophysics Data System (ADS)
Boon, N. J.; Hoyle, R. B.
2012-08-01
Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.
Coarse-grained protein molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Derreumaux, Philippe; Mousseau, Normand
2007-01-01
A limiting factor in biological science is the time-scale gap between experimental and computational trajectories. At this point, all-atom explicit solvent molecular dynamics (MD) are clearly too expensive to explore long-range protein motions and extract accurate thermodynamics of proteins in isolated or multimeric forms. To reach the appropriate time scale, we must then resort to coarse graining. Here we couple the coarse-grained OPEP model, which has already been used with activated methods, to MD simulations. Two test cases are studied: the stability of three proteins around their experimental structures and the aggregation mechanisms of the Alzheimer's 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.
Multiple branched adaptive steered molecular dynamics
NASA Astrophysics Data System (ADS)
Ozer, Gungor; Keyes, Thomas; Quirk, Stephen; Hernandez, Rigoberto
2014-08-01
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.
Dynamics of Nanoscale Grain-Boundary Decohesion in Aluminum by Molecular-Dynamics Simulation
NASA Technical Reports Server (NTRS)
Yamakov, V.; Saether, E.; Phillips, D. R.; Glaessegen, E. H.
2007-01-01
The dynamics and energetics of intergranular crack growth along a flat grain boundary in aluminum is studied by a molecular-dynamics simulation model for crack propagation under steady-state conditions. Using the ability of the molecular-dynamics simulation to identify atoms involved in different atomistic mechanisms, it was possible to identify the energy contribution of different processes taking place during crack growth. The energy contributions were divided as: elastic energy, defined as the potential energy of the atoms in fcc crystallographic state; and plastically stored energy, the energy of stacking faults and twin boundaries; grain-boundary and surface energy. In addition, monitoring the amount of heat exchange with the molecular-dynamics thermostat gives the energy dissipated as heat in the system. The energetic analysis indicates that the majority of energy in a fast growing crack is dissipated as heat. This dissipation increases linearly at low speed, and faster than linear at speeds approaching 1/3 the Rayleigh wave speed when the crack tip becomes dynamically unstable producing periodic dislocation bursts until the crack is blunted.
Integration methods for molecular dynamics \\Lambda Benedict J. Leimkuhler
Reich, Sebastian
Integration methods for molecular dynamics \\Lambda Benedict J. Leimkuhler Department of Mathematics approximation of a par ticular solution trajectory on meaningful time intervals is neither ob tainable nor
Dynamical effective potentials in electron tunneling
NASA Astrophysics Data System (ADS)
Maruši?, L.; Šunji?, M.
1993-12-01
Dynamical screening of electrons tunneling in the metal-insulator-metal system is treated generalizing the Jonson's nonlocal theory of exchange-correlation potential and the effective barrier concept. The self-energy is evaluated within the GW approximation for electrons coupled to the long-wavelength charge-density oscillations. Potentials are calculated self-consistently, and compared with non-self-consistent results, and those obtained within the local limit. We show that the concept of effective potential is valid only for electron energies below the top of the barrier, and for these energies there is usually no need for a self-consistent treatment. We also show that effective potential does not vary appreciably with electron energy when this energy is below the top of the barrier and far from the surface plasmon energies.
Molecular encryption and reconfiguration for remodeling of dynamic hydrogels.
Li, Shihui; Gaddes, Erin R; Chen, Niancao; Wang, Yong
2015-05-11
Dynamic materials have been widely studied for regulation of cell adhesion that is important to a variety of biological and biomedical applications. These materials can undergo changes mainly through one of the two mechanisms: ligand release in response to chemical, physical, or biological stimuli, and ligand burial in response to mechanical stretching or the change of electrical potential. This study demonstrates an encrypted ligand and a new hydrogel that are capable of inducing and inhibiting cell adhesion, which is controlled by molecular reconfiguration. The ligand initially exhibits an inert state; it can be reconfigured into active and inert states by using unblocking and recovering molecules in physiological conditions. Since molecular reconfiguration does not require the release of the ligand from the hydrogels, inhibiting and inducing cell adhesion on the hydrogels can be repeated for multiple cycles. PMID:25808026
Shock compression of hydrocarbon polymer foam using molecular dynamics
NASA Astrophysics Data System (ADS)
Lane, J. Matthew D.; Grest, Gary S.; Thompson, Aidan P.; Cochrane, Kyle R.; Desjarlais, Michael; Mattsson, Thomas R.
2012-03-01
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.
Kaczor, Agnieszka A; Targowska-Duda, Katarzyna M; Patel, Jayendra Z; Laitinen, Tuomo; Parkkari, Teija; Adams, Yahaya; Nevalainen, Tapio J; Poso, Antti
2015-10-01
The endocannabinoid system remains an attractive molecular target for pharmacological intervention due to its roles in the central nervous system in learning, thinking, emotional function, regulation of food intake or pain sensation, as well as in the peripheral nervous system, where it modulates the action of cardiovascular, immune, metabolic or reproductive function. ?/? hydrolase domain containing 6 (ABHD6)-an enzyme forming part of the endocannabinoid system-is a newly discovered post-genomic protein acting as a 2-AG (2-arachidonoylglycerol) serine hydrolase. We have recently reported a series of 1,2,5-thiadiazole carbamates as potent and selective ABHD6 inhibitors. Here, we present comparative molecular field analysis (CoMFA) and molecular dynamics studies of these compounds. First, we performed a homology modeling study of ABHD6 based on the assumption that the catalytic triad of ABHD6 comprises Ser148-His306-Asp 278 and the oxyanion hole is formed by Met149 and Phe80. A total of 42 compounds was docked to the homology model using the Glide module from the Schrödinger suite of software and the selected docking poses were used for CoMFA alignment. A model with the following statistics was obtained: R (2) = 0.98, Q (2) = 0.55. In order to study the molecular interactions of the inhibitors with ABHD6 in detail, molecular dynamics was performed with the Desmond program. It was found that, during the simulations, the hydrogen bond between the inhibitor carbonyl group and the main chain of Phe80 is weakened, whereas a new hydrogen bond with the side chain of Ser148 is formed, facilitating the possible formation of a covalent bond. Graphical Abstract Left-right: Docking pose of 1 in the binding pocket of ?/? hydrolase domain containing 6 (ABHD6) selected for molecular alignment; CoMFA steric and electrostatic contour fields; changes in potential energy of the complex during simulations for the complex of 6 and ABHD6. PMID:26350245
NASA Astrophysics Data System (ADS)
Alvarez, F.; Arbe, A.; Colmenero, J.
2000-11-01
We have carried out molecular dynamics (MD) simulations of polyisoprene at 363 K, about 150 K above the experimental glass transition temperature, using the INSIGHT and DISCOVER programs from MSI Inc. with the Polymer Consortium Force Field. The model system was built using the MSI amorphous cell construction protocol with periodic boundary conditions. Starting from the self part of the van Hove correlation function, the incoherent intermediate scattering function was calculated for the protons in the main chain and in the methyl groups (MGs). The dynamics of the latter ones can be well described assuming decoupled segmental dynamics and rotations in a threefold potential. The limits of such an approximation are also discussed. We find the existence of a distribution of potential barriers for MG rotation which is very similar to that deduced from low temperature (150 K) MD-simulation results and inelastic neutron scattering measurements. The glass transition would thus hardly modify this distribution.
Combining Optimal Control Theory and Molecular Dynamics for Protein Folding
Arkun, Yaman; Gur, Mert
2012-01-01
A new method to develop low-energy folding routes for proteins is presented. The novel aspect of the proposed approach is the synergistic use of optimal control theory with Molecular Dynamics (MD). In the first step of the method, optimal control theory is employed to compute the force field and the optimal folding trajectory for the atoms of a Coarse-Grained (CG) protein model. The solution of this CG optimization provides an harmonic approximation of the true potential energy surface around the native state. In the next step CG optimization guides the MD simulation by specifying the optimal target positions for the atoms. In turn, MD simulation provides an all-atom conformation whose positions match closely the reference target positions determined by CG optimization. This is accomplished by Targeted Molecular Dynamics (TMD) which uses a bias potential or harmonic restraint in addition to the usual MD potential. Folding is a dynamical process and as such residues make different contacts during the course of folding. Therefore CG optimization has to be reinitialized and repeated over time to accomodate these important changes. At each sampled folding time, the active contacts among the residues are recalculated based on the all-atom conformation obtained from MD. Using the new set of contacts, the CG potential is updated and the CG optimal trajectory for the atoms is recomputed. This is followed by MD. Implementation of this repetitive CG optimization - MD simulation cycle generates the folding trajectory. Simulations on a model protein Villin demonstrate the utility of the method. Since the method is founded on the general tools of optimal control theory and MD without any restrictions, it is widely applicable to other systems. It can be easily implemented with available MD software packages. PMID:22238629
Multiple ionization and fragmentation dynamics of molecular iodine studied in
Kling, Matthias
Multiple ionization and fragmentation dynamics of molecular iodine studied in IRXUV pump The ionization and fragmentation dynamics of iodine molecules (I2) are traced using very intense ($1014 W cmÀ2
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
Gottwald, Fabian; Ivanov, Sergei D; Kühn, Oliver
2015-01-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation (GLE), which can be rigorously derived by means of a linear projection (LP) technique. Within this framework a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here we discuss that this task is most naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importa...
Anisotropic magnetic molecular dynamics of cobalt nanowires
NASA Astrophysics Data System (ADS)
Beaujouan, David; Thibaudeau, Pascal; Barreteau, Cyrille
2012-11-01
An investigation of thermally induced spin and lattice dynamics of a cobalt nanowire on a (111)Pt substrate is presented via magnetic molecular dynamics. This dynamical simulation model treats each atom as a particle supporting a classical spin. A coordinate dependent on both exchange and anisotropic functions ensures a minimal coupling between the spin and the lattice degrees of freedom to translate the magnetostrictive behavior of most magnetic materials. A spin-pair model of anisotropy is proposed to connect to the lattice thermodynamics. In order to solve linked spin-coordinate equations of motion, the efficiencies of algorithms based on Suzuki-Trotter decompositions are compared. The temperature dependence of the magnetic behavior of Co nanowires is investigated through thermal stochastic connections with mechanical and spin Langevin noises. From a magnetic Hamiltonian parametrized on ab initio calculations, the size dependence of the energy barriers and characteristic time scales of the magnetization relaxation are computed. In the superparamagnetic limit, it is shown that all spins in a nanowire evolve in a coherent rotation. When the size of the single nanowire increases, nucleations of domain walls let the activation energy be independent of the length of the wire.
R. E. Ryltsev; N. M. Chtchelkatchev; V. N. Ryzhov
2013-01-09
We investigate glassy dynamical properties of one component three-dimensional system of particles interacting via pair repulsive potential by the molecular dynamic simulation in the wide region of densities. The glass state is superfragile and it has high glassforming ability. The glass transition temperature Tg has pronounced minimum at densities where the frustration is maximal.
Singh, S.B.
1992-01-01
The structures of the adducts of (+)- and (-)trans-7,8,dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo (a)pyrene (anti-BPDE) formed by trans addition to N[sup 2] of guanine have been of great interest because the high biological activity of BPDE in mammalian mutagenesis and tumorigenesis has been attributed to the predominant (+)-adduct, while the (-)-adduct is inactive. Molecular mechanics and dynamics calculations have been employed to elucidate the structural difference between this mirror image adduct pair in a duplex dodecamer, d(5' GCGCGCG-(BPDE)CGCGC3') [center dot] d(5'GCGCGCGCGCGC3'). Minimized potential energy calculations using the program DUPLEX were employed to locate starting structures for the dynamics. Three types of structures were found in the energy minimized conformation space searches for each enantiomer: pyrenyl moiety in the minor groove of a Watson-Crick base paired B-DNA duplex, pyrenyl moiety in the major groove of a B-DNA duplex with syn guanine and Hoogsteen base pairs at the modification site, and intercalation type structures. The minor groove structure is energetically preferred for the (+) enantiomer while both minor groove and major groove structures are favored and of comparable energy in the (-) enantiomer. These energy-minimized duplex dodecamers, as well as an unmodified B-DNA control of the same sequence, were subjected to 100 ps molecular dynamics simulations with solvent and salt with the program AMBER. The duplex dodecamer, d(CGCGAATTCGCG)[sub 2], was subjected to a similar simulation using the crystal structure as starting coordinates. Detailed analysis of the dynamic evolution of the conformational and the helical parameters of all the dodecamer simulations were carried out with Molecular Dynamics Analysis Toolchest.
Dynamic transitions in molecular dynamics simulations of supercooled silicon
NASA Astrophysics Data System (ADS)
Mei, Xiaojun; Eapen, Jacob
2013-04-01
Two dynamic transitions or crossovers, one at a low temperature (T* ? 1006 K) and the other at a high temperature (T0 ? 1384 K), are shown to emerge in supercooled liquid silicon using molecular dynamics simulations. The high-temperature transition (T0) marks the decoupling of stress, density, and energy relaxation mechanisms. At the low-temperature transition (T*), depending on the cooling rate, supercooled silicon can either undergo a high-density-liquid to low-density-liquid (HDL-LDL) phase transition or experience an HDL-HDL crossover. Dynamically heterogeneous domains that emerge with supercooling become prominent across the HDL-HDL transition at 1006 K, with well-separated mobile and immobile regions. Interestingly, across the HDL-LDL transition, the most mobile atoms form large prominent aggregates while the least mobile atoms get spatially dispersed akin to that in a crystalline state. The attendant partial return to spatial uniformity with the HDL-LDL phase transition indicates a dynamic mechanism for relieving the frustration in supercooled states.
Atomistic Molecular Dynamics Simulations of the Electrical Double
NASA Astrophysics Data System (ADS)
Li, Zifeng; Milner, Scott; Fichthorn, Kristen
2015-03-01
The electrical double layer (EDL) near the polymer/water interface plays a key role in the colloidal stability of latex paint. To elucidate the structure of the EDL at the molecular level, we conducted an all-atom molecular dynamics simulations. We studied two representative surface charge groups in latex, the ionic surfactant sodium dodecyl sulfate (SDS) and the grafted short polyelectrolyte charged by dissociated methyl methacrylic acid (MAA) monomers. Our results confirm that the Poisson-Boltzmann theory works well outside the Stern layer. Our calculated electrostatic potential at the Outer Helmholtz Plane (OHP) is close to the zeta potential measured experimentally, which suggests that the potential at the OHP is a good estimate of the zeta potential. We found that the position of the OHP for the MAA polyelectrolyte system extends much further into the aqueous phase than that in the SDS system, resulting in a Stern layer that is twice as thick. This model will allow for future investigations of the interactions of the surface with different surfactants and rheology modifiers, which may serve as a guide to tune the rheology of latex formulations. We thank Dow Chemical Company for financial support.
Molecular Dynamics Simulation on Stability of Insulin on Graphene
NASA Astrophysics Data System (ADS)
Liang, Li-jun; Wang, Qi; Wu, Tao; Shen, Jia-wei; Kang, Yu
2009-12-01
The adsorption dynamics of a model protein (the human insulin) onto graphene surfaces with different sizes was investigated by molecular dynamics simulations. During the adsorption, it has different effect on the stability of the model protein in the fixed and non-fixed graphene systems. The tertiary structure of the protein was destroyed or partially destroyed, and graphene surfaces shows the selective protection for some ?-helices in non-fixed systems but not in fixed systems by reason of the flexibility of graphene. As indicated by the interaction energy curve and trajectory animation, the conformation and orientation selection of the protein were induced by the properties and the texture of graphene surfaces. The knowledge of protein adsorption on graphene surfaces would be helpful to better understand stability of protein on graphene surfaces and facilitate potential applications of graphene in biotechnology.
Ion Mobility Analysis of Molecular Dynamics
NASA Astrophysics Data System (ADS)
Wyttenbach, Thomas; Pierson, Nicholas A.; Clemmer, David E.; Bowers, Michael T.
2014-04-01
The combination of mass spectrometry and ion mobility spectrometry (IMS) employing a temperature-variable drift cell or a drift tube divided into sections to make IMS-IMS experiments possible allows information to be obtained about the molecular dynamics of polyatomic ions in the absence of a solvent. The experiments allow the investigation of structural changes of both activated and native ion populations on a timescale of 1&-100 ms. Five different systems representing small and large, polar and nonpolar molecules, as well as noncovalent assemblies, are discussed in detail: a dinucleotide, a sodiated polyethylene glycol chain, the peptide bradykinin, the protein ubiquitin, and two types of peptide oligomers. Barriers to conformational interconversion can be obtained in favorable cases. In other cases, solution-like native structures can be observed, but care must be taken in the experimental protocols. The power of theoretical modeling is demonstrated.
Assessing Molecular Dynamics Simulations with Solvatochromism Modeling.
Schwabe, Tobias
2015-08-20
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied. PMID:26220273
Nonequilibrium molecular dynamics: The first 25 years
Hoover, W.G. [Univ. of California, Davis, CA (United States); [Lawrence Livermore National Lab., CA (United States)
1992-08-01
Equilibrium Molecular Dynamics has been generalized to simulate Nonequilibrium systems by adding sources of thermodynamic heat and work. This generalization incorporates microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress, and augments atomistic forces with special boundary, constraint, and driving forces capable of doing work on, and exchanging heat with, an otherwise Newtonian system. The underlying Lyapunov instability of these nonequilibrium equations of motion links microscopic time-reversible deterministic trajectories to macroscopic time-irreversible hydrodynamic behavior as described by the Second Law of Thermodynamics. Green-Kubo linear-response theory has been checked. Nonlinear plastic deformation, intense heat conduction, shockwave propagation, and nonequilibrium phase transformation have all been simulated. The nonequilibrium techniques, coupled with qualitative improvements in parallel computer hardware, are enabling simulations to approximate real-world microscale and nanoscale experiments.
Molecular dynamics simulations of lithium alkyl carbonates.
Borodin, Oleg; Smith, Grant D; Fan, Peng
2006-11-16
A quantum chemistry-based many-body polarizable force field has been developed for two model solid-electrolyte interphase (SEI) components: dilithium ethylene dicarbonate (Li(2)EDC) and lithium methyl carbonate (LiMC). Molecular dynamics (MD) simulations of amorphous Li(2)EDC and LiMC were performed at temperatures from 393 to 600 K. Simulations reveal that Li(+) is coordinated by approximately 4.6 oxygen atoms from -COO(-) groups coming from different alkyl carbonate molecules. Charge transport in Li(2)EDC was found to be almost entirely due to Li(+). The temperature dependence of the ionic conductivity of the SEI model compounds Li(2)EDC and LiMC was found to be significantly stronger than that of liquid electrolytes (e.g., ethylene carbonate + LiTFSI), yielding extrapolated conductivities of the Li(2)EDC on order of 10(-10) S/cm at -30 degrees C. PMID:17092027
Molecular Dynamics Simulation of the Association of Nonpolar Spheres in Water
E. Spohr; D. Henderson
2002-01-01
We apply molecular dynamics (MD) simulations to the study of the association of nonpolar spheres of effective radii between 1.6 and 6.1 Å dissolved in water. The constrained MD method is used to calculate the potential of mean force (PMF) of the interaction between spheres. The depth of the potential of mean force increases with increasing radius of the nonpolar
Kling, Matthias
2010-01-01
PHYSICAL REVIEW A 82, 013408 (2010) Tracking nuclear wave-packet dynamics in molecular oxygen ions have tracked nuclear wave-packet dynamics in doubly charged states of molecular oxygen using few observed. The occurrence of vibrational revivals permits us to identify the potential curves of the O2
A Hands-On Introduction to Molecular Dynamics
NASA Astrophysics Data System (ADS)
Lamberti, Vincent E.; Fosdick, Lloyd D.; Jessup, Elizabeth R.; Schauble, Carolyn J. C.
2002-05-01
We present an introduction to the chemical and computational aspects of the molecular dynamics (MD) simulation technique. Using just a few elementary ideas from classical mechanics and numerical analysis, and linear chains of identical particles as example systems, we take the reader through the steps required for the design and analysis of a simple molecular dynamics experiment. We employ the Hooke's law model for the interactions between the particles since its visualization in terms of masses and springs provides a natural model for chemical bonds. We derive the classical equations of motion in detail for the three-particle chain. We then introduce two simple methods for numerically integrating the equations of motion, one based on Euler's method for differential equations, and the other a more accurate algorithm developed by Verlet. We analyze the dynamics of the three-particle system in terms of its normal modes of vibration. Finally, exploiting the closed-form solution admitted by the Hooke's law potential, we compare the errors generated by the two integration algorithms. As supplemental material, we provide a basic MD implementation using the Euler algorithm in both Fortran and C and a set of suggested exercises.
Statistical Analysis of Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Atkinson, R. A.
Available from UMI in association with The British Library. Requires signed TDF. This thesis is concerned with the specification and analysis of stochastic models of molecular motion and interaction in simple liquids. Basic chemical terminology is introduced and a brief description is given of the technique of molecular dynamics simulation. Stochastic process theory, in so far as it is relevant to the modelling of molecular trajectories and chemical reaction, is reviewed. First passage densities are shown to be important in the analysis of diffusion controlled chemical reaction. The relationship between first passage densities and flux or flow across the absorbing boundary is given. A formula proposed by Durbin is discussed and shown to be valid for diffusion processes under certain regularity conditions. The simplest integrated diffusion, integrated Brownian motion, is considered and a detailed derivation of McKean's half-winding formula is given. An explicit expression for the return-time density is derived, from which the large time asymptotics can be deduced. Goldman's formula for the density of the hitting-time of positive levels is extended to all real values and a simple intuitive derivation is given. Similar arguments enable the results of Gor'kov to be extended to a wider class of integrated diffusions. First passage time densities are computed numerically using the extension of Goldman's formula and compared with approximations which have been suggested by Hesse. Small drift asymptotics are derived for the escape probability of integrated Brownian motion with drift. A number of results are obtained for the integrated Ornstein -Uhlenbeck process, by using martingale methods. Finally, the empirical observations of Lynden-Bell, Hutchinson and Doyle are analysed. A stochastic model of single-particle motion based on the velocity autocorrelation function is proposed and shown to be in excellent agreement with the computer generated data.
Fractal and complex network analyses of protein molecular dynamics
NASA Astrophysics Data System (ADS)
Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Zhi-Qin; Anh, Vo
2014-12-01
Based on protein molecular dynamics, we investigate the fractal properties of energy, pressure and volume time series using the multifractal detrended fluctuation analysis (MF-DFA) and the topological and fractal properties of their converted horizontal visibility graphs (HVGs). The energy parameters of protein dynamics we considered are bonded potential, angle potential, dihedral potential, improper potential, kinetic energy, Van der Waals potential, electrostatic potential, total energy and potential energy. The shape of the h(q) curves from MF-DFA indicates that these time series are multifractal. The numerical values of the exponent h(2) of MF-DFA show that the series of total energy and potential energy are non-stationary and anti-persistent; the other time series are stationary and persistent apart from series of pressure (with H?0.5 indicating the absence of long-range correlation). The degree distributions of their converted HVGs show that these networks are exponential. The results of fractal analysis show that fractality exists in these converted HVGs. For each energy, pressure or volume parameter, it is found that the values of h(2) of MF-DFA on the time series, exponent ? of the exponential degree distribution and fractal dimension dB of their converted HVGs do not change much for different proteins (indicating some universality). We also found that after taking average over all proteins, there is a linear relationship between
How Dynamic Visualization Technology Can Support Molecular Reasoning
ERIC Educational Resources Information Center
Levy, Dalit
2013-01-01
This paper reports the results of a study aimed at exploring the advantages of dynamic visualization for the development of better understanding of molecular processes. We designed a technology-enhanced curriculum module in which high school chemistry students conduct virtual experiments with dynamic molecular visualizations of solid, liquid, and…
Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers
Goddard III, William A.
131 Chapter 7 Molecular Dynamics Simulations of Fluoro Polymers: Prediction of Glass Transition for molecular dynamics simulation of the uoro polymers: Polytetra uoroethylene PTFE, Polyvinylidene uoride PVDF using a Build-Anneal-Quench procedure. For PTFE, PVDF, and ETFE uoro polymers, these results predict
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
Donald Hamelberg; César Augusto F. de Oliveira; J. Andrew McCammon
2007-01-01
Slow diffusive conformational transitions play key functional roles in biomolecular systems. Our ability to sample these motions with molecular dynamics simulation in explicit solvent is limited by the slow diffusion of the solvent molecules around the biomolecules. Previously, we proposed an accelerated molecular dynamics method that has been shown to efficiently sample the torsional degrees of freedom of biomolecules beyond
Molecular dynamics of detonation in crystals with defects
Lee Phillips; Robert S. Sinkovits
1992-01-01
We examined, using computational molecular dynamics, shocks produced in two- and three dimensional atomic and molecular crystals through impact and end loading. The effect of various lattice defects on the shock propagation and the transition to detonation is investigated. It is observed that small defects in the lattice structure have a large effect on the shock and detonation dynamics. Intermolecular
Discrete Molecular Dynamics Study of Alzheimer Amyloid -protein (A) Folding
Stanley, H. Eugene
. 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
A molecular dynamics simulation of droplet evaporation Lorenzo Consolini 1
Aggarwal, Suresh K.
is relatively low, followed by nearly constant liquid- temperature evaporation at a ``pseudo wetA 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
Nonequilibrium Molecular Dynamics Simulation of Electric Conduction Tatsuro YUGE
Shimizu, Akira
simulation of heat conduction encourages us to study electric conduction using MD simulation of a mechanicalNonequilibrium Molecular Dynamics Simulation of Electric Conduction Tatsuro YUGE Ã , Nobuyasu ITO1y for electric conduction, and study transport phenomena by molecular dynamics simulation. We observe
Molecular dynamics simulations of boronnitride nanotubes embedded in
Burstedde, Carsten
Molecular dynamics simulations of boronnitride nanotubes embedded in amorphous SiBN Michael In this article, we examine the elastic properties of boronnitride nanotubes, which are embedded in amorphous siliconboronnitride ceramics. We employ molecular dynamics simulations using the Parrinello
Dynamic Load Balancing for the Distributed Mining of Molecular Structures
Berthold, Michael R.
Dynamic Load Balancing for the Distributed Mining of Molecular Structures Giuseppe Di Fatta, Member, IEEE, and Michael R. Berthold, Senior Member, IEEE Abstract--In molecular biology, it is often a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular
Molecular dynamics simulation in virus research
Ode, Hirotaka; Nakashima, Masaaki; Kitamura, Shingo; Sugiura, Wataru; Sato, Hironori
2012-01-01
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique. PMID:22833741
Molecular and chemical engineering of bacteriophages for potential medical applications.
Hodyra, Katarzyna; D?browska, Krystyna
2015-04-01
Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology. PMID:25048831
Large Scale Molecular Dynamics Simulations with Fast Multipole Implementations
Zhiqiang Wang; JAMES A. LUPO; ALAN M. MCKENNEY; RUTH PACHTER
1999-01-01
We present the performance of the fast molecular dynamics (FMD) code designed for efficient, object-oriented, and scalable large scale molecular simulations. FMD uses an implementation of the three-dimensional fast multipole method, FMM3D, developed in our group. The Fast Multipole Method offers an efficient way (order O(N)) to handle long range electrostatic interactions, thus enabling a more realistic molecular dynamics simulation
Large scale molecular dynamics simulations with fast multipole implementations
Zhiqiang Wang; James A. Lupo; Alan M. McKenney; Ruth Pachter
1999-01-01
We present the performance of the fast molecular dynamics (FMD) code designed for efficient, object-oriented, and scalable large scale molecular simulations. FMD uses an implementation of the three-dimensional fast multipole method, FMM3D, developed in our group. The Fast Multipole Method offers an efficient way (order O(N )) to handle long range electrostatic interactions, thus enabling a more realistic molecular dynamics
Multimillion atom molecular dynamics simulations of glasses and ceramic materials
Vashishta, Priya [Concurrent Computing Laboratory for Materials Simulations, Department of Physics and Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States); Kalia, Rajiv K. [Concurrent Computing Laboratory for Materials Simulations, Department of Physics and Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States); Nakano, Aiichiro [Concurrent Computing Laboratory for Materials Simulations, Department of Physics and Astronomy and Department of Computer Science, Louisiana State University, Baton Rouge, Louisiana 70803-4001 (United States)
1999-11-01
Molecular dynamics simulations are a powerful tool for studying physical and chemical phenomena in materials. In these lectures we shall review the molecular dynamics method and its implementation on parallel computer architectures. Using the molecular dynamics method we will study a number of materials in different ranges of density, temperature, and uniaxial strain. These include structural correlations in silica glass under pressure, crack propagation in silicon nitride films, sintering of silicon nitride nanoclusters, consolidation of nanophase materials, and dynamic fracture. Multimillion atom simulations of oxidation of aluminum nanoclusters and nanoindentation in silicon nitride will also be discussed. (c) 1999 American Institute of Physics.
Molecular Dynamics Simulations of Polyelectrolyte Solutions
NASA Astrophysics Data System (ADS)
Dobrynin, Andrey
2014-03-01
Polyelectrolytes are polymers with ionizable groups. In polar solvents, these groups dissociate releasing counterions into solution and leaving uncompensated charges on the polymer backbone. Examples of polyelectrolytes include biopolymers such as DNA and RNA, and synthetic polymers such as poly(styrene sulfonate) and poly(acrylic acids). In this talk I will discuss recent molecular dynamics simulations of static and dynamic properties of polyelectrolyte solutions. These simulations show that in dilute and semidilute polyelectrolyte solutions the electrostatic induced chain persistence length scales with the solution ionic strength as I - 1 / 2. This dependence of the chain persistence length is due to counterion condensation on the polymer backbone. In dilute polyelectrolyte solutions the chain size decreases with increasing the salt concentration as R ~ I- 1 / 5. This is in agreement with the scaling of the chain persistence length on the solution ionic strength, lp ~ I- 1 / 2. In semidilute solution regime at low salt concentrations the chain size decreases with increasing polymer concentration, R ~ cp-1 / 4 . While at high salt concentrations one observes a weaker dependence of the chain size on the solution ionic strength, R ~ I- 1 / 8. Analysis of the simulation data throughout the studied salt and polymer concentration ranges shows that there exist general scaling relations between multiple quantities X (I) in salt solutions and corresponding quantities X (I0) in salt-free solutions, X (I) = X (I0) (I /I0) ? . The exponent ? = -1/2 for chain persistence length lp , ? = 1/4 for solution correlation length, ? = -1/5 and ? = -1/8 for chain size R in dilute and semidilute solution regimes respectively. Furthermore, the analysis of the spectrum and of the relaxation times of Rouse modes confirms existence of the single length scale (correlation length) that controls both static and dynamic properties of semidilute polyelectrolyte solutions. These findings confirm predictions of the scaling model of polyelectrolyte solutions. NSF DMR-1004576.
The MOLDY short-range molecular dynamics package
NASA Astrophysics Data System (ADS)
Ackland, G. J.; D'Mellow, K.; Daraszewicz, S. L.; Hepburn, D. J.; Uhrin, M.; Stratford, K.
2011-12-01
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.
Shojaei, S H Reza; Vandenbussche, Jelle; Deleuze, Michael S; Bultinck, Patrick
2013-09-01
The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules. PMID:23902590
Molecular Mechanisms and Potential Therapeutical Targets in Huntington's Disease
Brutlag, Doug
Molecular Mechanisms and Potential Therapeutical Targets in Huntington's Disease CHIARA ZUCCATO to Huntington's Disease 906 A. Historical background 906 B. Neuropathology 907 C. Symptoms 908 D. Gene hunters VII. Targeting Cell Loss: Cell Replacement Approaches 956 VIII. Biomarkers in Huntington's Disease 957
Identification of potential biophysical and molecular signalling mechanisms
Athanasiou, Kyriacos
of exogenous hyaluronic acid (HA) on the biomechanical and biochemical properties of self-assembled bovineIdentification of potential biophysical and molecular signalling mechanisms underlying hyaluronic acid enhancement of cartilage formation Donald J. Responte1,3, Roman M. Natoli2 and Kyriacos A
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 ...
Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility
Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility motions of altitudinal molecular rotors using molecular dynamics (MD) computer simulations based surfaces act as thermally- or mechanically activated molecular rotors, although the mechanisms
Molecular dynamics in cytochrome c oxidase Moessbauer spectra deconvolution
Bossis, Fabrizio; Palese, Luigi L.
2011-01-07
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.
Modeling Of Blood Vessel Constriction In 2-D Case Using Molecular Dynamics Method
Mohamad Rendi; Suprijadi; Sparisoma Viridi
2013-06-25
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80 % constriction, which shows existence of maximum pressure that can be overcome by vessel wall.
Modeling of blood vessel constriction in 2-D case using molecular dynamics method
NASA Astrophysics Data System (ADS)
A. S., M. Rendi; Suprijadi, Viridi, S.
2014-03-01
Blood vessel constriction is simulated with particle-based method using a molecular dynamics authoring software known as Molecular Workbench (WM). Blood flow and vessel wall, the only components considered in constructing a blood vessel, are all represented in particle form with interaction potentials: Lennard-Jones potential, push-pull spring potential, and bending spring potential. Influence of medium or blood plasma is accommodated in plasma viscosity through Stokes drag force. It has been observed that pressure p is increased as constriction c is increased. Leakage of blood vessel starts at 80% constriction, which shows existence of maximum pressure that can be overcome by vessel wall.
NASA Astrophysics Data System (ADS)
Ji, Pengfei; Zhang, Yuwen; Yang, Mo
2013-12-01
The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
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
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.
Modeling and Bio molecular Self-assembly via Molecular Dynamics and Dissipative Particle Dynamics
NASA Astrophysics Data System (ADS)
Rakesh, L.
2009-09-01
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.
Oxidation dynamics of nanophase aluminum clusters : a molecular dynamics study.
Ogata, S.
1998-01-27
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. We find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28{angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Oxidation dynamics of nanophase aluminum clusters: A molecular dynamics study
Ogata, Shuji [Yamaguchi Univ., Ube (Japan). Dept. of Applied Sciences; Campbell, T.J.; Tsuruta, Kenji; Nakano, Aiichiro; Kalia, R.K.; Vashishta, P. [Louisiana State Univ., Baton Rouge, LA (United States); Loong, C.K. [Argonne National Lab., Baton Rouge, LA (United States)
1998-12-31
Oxidation of an aluminum nanocluster (252,158 atoms) of radius 100{angstrom} placed in gaseous oxygen (530,727 atoms) is investigated by performing molecular-dynamics simulations on parallel computers. The simulation takes into account the effect of charge transfer between Al and O based on the electronegativity equalization principles. The authors find that the oxidation starts at the surface of the cluster and the oxide layer grows to a thickness of {approximately}28 {angstrom}. Evolutions of local temperature and densities of Al and O are investigated. The surface oxide melts because of the high temperature resulting from the release of energy associated with Al-O bondings. Amorphous surface-oxides are obtained by quenching the cluster. Vibrational density-of-states for the surface oxide is analyzed through comparisons with those for crystalline Al, Al nanocluster, and {alpha}-Al{sub 2}O{sub 3}.
Gas-Phase Molecular Dynamics: Vibrational Dynamics of Polyatomic Molecules
Muckerman, J.T.
1999-05-21
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high- temperature, flow-tube reaction kinetics studies with mass-spectrometic sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and in turn, provide new tools for the study of energy flow and chemical bond cleavage in the radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.
GAS-PHASE MOLECULAR DYNAMICS: VIBRATIONAL DYNAMICS OF POLYATOMIC MOLECULES
MUCKERMAN,J.T.
1999-06-09
The goal of this research is the understanding of elementary chemical and physical processes important in the combustion of fossil fuels. Interest centers on reactions and properties of short-lived chemical intermediates. High-resolution, high-sensitivity, laser absorption methods are augmented by high-temperature, flow-tube reaction kinetics studies with mass-spectrometric sampling. These experiments provide information on the energy levels, structures and reactivity of molecular free radical species and, in turn, provide new tools for the study of energy flow and chemical bond cleavage in radicals involved in chemical systems. The experimental work is supported by theoretical studies using time-dependent quantum wavepacket calculations, which provide insight into energy flow among the vibrational modes of polyatomic molecules and interference effects in multiple-surface dynamics.
Detection and Visualization of Anomalous Structures in Molecular Dynamics Simulation Data
Wilkins, John
Detection and Visualization of Anomalous Structures in Molecular Dynamics Simulation Data Sameep we explore techniques to detect and visualize features in data from molecular dynamics (MD Extraction, Scientific Data Visualization, Data Mining, iso-surface, Transfer Functions, Molecular Dynamics
Internal coordinate molecular dynamics: a foundation for multiscale dynamics.
Vaidehi, Nagarajan; Jain, Abhinandan
2015-01-29
Internal coordinates such as bond lengths, bond angles, and torsion angles (BAT) are natural coordinates for describing a bonded molecular system. However, the molecular dynamics (MD) simulation methods that are widely used for proteins, DNA, and polymers are based on Cartesian coordinates owing to the mathematical simplicity of the equations of motion. However, constraints are often needed with Cartesian MD simulations to enhance the conformational sampling. This makes the equations of motion in the Cartesian coordinates differential-algebraic, which adversely impacts the complexity and the robustness of the simulations. On the other hand, constraints can be easily placed in BAT coordinates by removing the degrees of freedom that need to be constrained. Thus, the internal coordinate MD (ICMD) offers an attractive alternative to Cartesian coordinate MD for developing multiscale MD method. The torsional MD method is a special adaptation of the ICMD method, where all the bond lengths and bond angles are kept rigid. The advantages of ICMD simulation methods are the longer time step size afforded by freezing high frequency degrees of freedom and performing a conformational search in the more important low frequency torsional degrees of freedom. However, the advancements in the ICMD simulations have been slow and stifled by long-standing mathematical bottlenecks. In this review, we summarize the recent mathematical advancements we have made based on spatial operator algebra, in developing a robust long time scale ICMD simulation toolkit useful for various applications. We also present the applications of ICMD simulations to study conformational changes in proteins and protein structure refinement. We review the advantages of the ICMD simulations over the Cartesian simulations when used with enhanced sampling methods and project the future use of ICMD simulations in protein dynamics. PMID:25517406
Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.
Graziani, F R; Bauer, J D; Murillo, M S
2014-09-01
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
NASA Astrophysics Data System (ADS)
Banuelos, E. U.; Amarillas, A. P.
2004-02-01
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.
Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Paquet, Eric; Viktor, Herna L.
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.
Paquet, Eric; Viktor, Herna L
2015-01-01
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods. PMID:25785262
Can the ring polymer molecular dynamics method be interpreted as real time quantum dynamics?
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
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.
Molecular Biology of Gallbladder Cancer: Potential Clinical Implications
Andrén-Sandberg, Åke
2012-01-01
Gallbladder cancer (GBC) is a common malignancy of the biliary tract and involves the changes in multiple oncogenes and multiple genetic genes. Since over the past decade there has been an advance in the knowledge of the genetic basis of cancer, mainly as a result of the rapid progression of molecular technology; however, conventional therapeutic approaches have not had much impact on the course of this aggressive neoplasm. Knowledge of the molecular biology of GBC is rapidly growing. Genetic alterations in GBC include adenosine triphosphate-binding cassette transporter ABCG8, membrane-bound enzyme ADAM-17 of multi-functional gene family, and other genes including p53, COX2, XPC, and RASSF1A. The advances in molecular biology have potential implications for the detection of this disease, using Synuclein-gamma, Syndecan-1, glycoprotein 72 (TAG-72), tumor endothelial marker 8 protein (TEM8) and TNF-alpha. The use of these molecular diagnostic methods is of clinical importance for the gene replacement therapy, genetic prodrug activation therapy, and antisense immunology technology for the treatment of malignancy. The author reviewed recent publications on PubMed, and summarized molecular biology of GBC, with an emphasis on features of potential clinical implications for diagnosis and management. PMID:23112962
NASA Astrophysics Data System (ADS)
Anil Kumar, A. V.
2014-07-01
The dynamics of a binary colloidal mixture under the influence of an external potential barrier has been studied by molecular dynamics simulations. The attractive depletion interaction between the barrier and larger particles fastens the dynamics of the larger particles over the potential barrier. At low temperatures, depletion interactions cause the larger particles to diffuse faster than smaller particles, which is counterintuitive. The repulsive barrier leads the small particles to undergo an anomalous diffusion which resembles the dynamics of systems undergoing a glass transition, while the larger particles undergo normal diffusion even at very low temperature.
Anil Kumar, A V
2014-07-21
The dynamics of a binary colloidal mixture under the influence of an external potential barrier has been studied by molecular dynamics simulations. The attractive depletion interaction between the barrier and larger particles fastens the dynamics of the larger particles over the potential barrier. At low temperatures, depletion interactions cause the larger particles to diffuse faster than smaller particles, which is counterintuitive. The repulsive barrier leads the small particles to undergo an anomalous diffusion which resembles the dynamics of systems undergoing a glass transition, while the larger particles undergo normal diffusion even at very low temperature. PMID:25053339
Molecular Dynamics Simulation of Fluid Systems.
NASA Astrophysics Data System (ADS)
Sun, Mingqiu
In this dissertation, we use molecular dynamics simulations to study several interesting phenomena in fluid systems. Some novel computational techniques are also introduced, including the use of dynamic linked lists, a method for simulating cellular automata, and a numerical diffraction method for visualizing crystal structures. Firstly, we study compressible fluid flow in narrow two-dimensional channels. In the simulation area, an upstream source is maintained at constant density and temperature while a downstream reservoir is kept at vacuum. A novel wall model, incorporating the effects of inelastic collisions between fluid and wall molecules, molecular structure of the wall, and a long-ranged fluid-wall interaction, is used in these simulations. We find that the velocity distribution differs significantly from a parabolic profile close to the walls. Also, for a sufficiently strong fluid-wall attraction the fluid velocity goes smoothly to zero at the wall, indicating the absence of velocity slip. As the fluid becomes more rarefied, the flow velocity goes to zero at the wall increasingly sharply in an increasingly narrow region, behavior which could be interpreted as velocity slip. These results are different from those of the usual kinetic theory of fluid flow at walls and also from the predictions of the Chapman-Enskog method. They are, however, in qualitative agreement with the non-linear theory of Eu. In the second system we study, instead of inducing flow with a pressure or density gradient, we drive an external temperature gradient across the system to simulate a directional solidification process. A solid is formed as the externally imposed temperature gradient is pulled across a sample which is initially in the liquid phase. If the solid-liquid interface moves more slowly than the pulling speed, the initially flat interface develops large sinusoidal irregularities when the tail of the external temperature gradient passes the moving interface. We identify the instability as a Mullins-Sekerka type, arising from the density gradient in the liquid phase which is in turn a consequence of the density difference between the solid and liquid phases.
Molecular Dynamics Simulation of Temperature Relaxation in Dense Hydrogen Plasma
NASA Astrophysics Data System (ADS)
Zhao, Zengxiu; Ma, Qian; Dai, Jiayu; Kang, Dongdong; Yuan, Jianmin
2013-10-01
Temperature relaxation between electrons and ions in dense plasma is regarded as an essential factor in understanding the physics process in laser-plasma interactions. Here, we perform molecular dynamics (MD) simulation to investigate the electron-ion temperature relaxation with semi-classical potentials in fully ionized dense hydrogen plasma. We compare the results of different potentials such as HM potential, Yukawa potential and Coulomb potential with an appropriate cutoff, in addition, a simplified scattering model is used in the MD simulation to overcome the negative effect called Coulomb Catastrophe. The MD simulation is performed with a code using velocity Verlet integration in a box cell with periodic boundary and the electron number density changes from to. The tested particle number N is ranging from N = 500 to as many as N = 4000, the results reported here use N = 1372. Statistical uncertainty for each case is estimated by performing the code from 6 samples of the ensemble and then taking the average and standard deviation. Furthermore, the results of theoretical models, such as LS, GMS and BPS, are also used to compare with the MD results.
A new shared-memory programming paradigm for molecular dynamics simulations on the Intel Paragon
D`Azevedo, E.F.; Romine, C.H.
1994-12-01
This report describes the use of shared memory emulation with DOLIB (Distributed Object Library) to simplify parallel programming on the Intel Paragon. A molecular dynamics application is used as an example to illustrate the use of the DOLIB shared memory library. SOTON-PAR, a parallel molecular dynamics code with explicit message-passing using a Lennard-Jones 6-12 potential, is rewritten using DOLIB primitives. The resulting code has no explicit message primitives and resembles a serial code. The new code can perform dynamic load balancing and achieves better performance than the original parallel code with explicit message-passing.
Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations
Cai, Wei
Plasticity of metal wires in torsion: Molecular dynamics and dislocation dynamics simulations t The orientation dependent plasticity in metal nanowires is investigated using molecular dynamics and dislocation wires controls the mechanisms of plastic deformation. For wires oriented along /1 1 0S, dislocations
Dynamic Structure Factors from Lipid Membrane Molecular Dynamics Simulations
Brandt, Erik G.; Edholm, Olle
2009-01-01
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
Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D.; Kühn, Oliver
2015-06-01
Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied, usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.
Molecular Dynamics Simulation of Binary Fluid in a Nanochannel
Mullick, Shanta; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, SummerHill, Shimla - 171005 (India); Pathania, Y. [Chitkara University, Atal Shiksha Kunj, Atal Nagar, Barotiwala, Dist Solan, Himachal Pradesh - 174103 (India)
2011-12-12
This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12{sigma}, 14{sigma} and 16{sigma} and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.
Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Laghaei, Rozita; Mousseau, Normand
2010-04-01
Expansion of polyglutamine (polyQ) beyond the pathogenic threshold (35-40 Gln) is associated with several neurodegenerative diseases including Huntington's disease, several forms of spinocerebellar ataxias and spinobulbar muscular atrophy. To determine the structure of polyglutamine aggregates we perform replica-exchange molecular dynamics simulations coupled with the optimized potential for effective peptide forcefield. Using a range of temperatures from 250 to 700 K, we study the aggregation kinetics of the polyglutamine monomer and dimer with chain lengths from 30 to 50 residues. All monomers show a similar structural change at the same temperature from ?-helical structure to random coil, without indication of any significant ?-strand. For dimers, by contrast, starting from random structures, we observe spontaneous formation of antiparallel ?-sheets and triangular and circular ?-helical structures for polyglutamine with 40 residues in a 400 ns 50 temperature replica-exchange molecular dynamics simulation (total integrated time 20 ?s). This ˜32 Å diameter structure reorganizes further into a tight antiparallel double-stranded ˜22 Å nanotube with 22 residues per turn close to Perutz' model for amyloid fibers as water-filled nanotubes. This diversity of structures suggests the existence of polymorphism for polyglutamine with possibly different pathways leading to the formation of toxic oligomers and to fibrils.
Molecular dynamics simulations of water and ion dynamics in the electrochemical double layer
E. Spohr
2002-01-01
The application of molecular dynamics (MD) simulations of the interface between an aqueous electrolyte solution and a solid surface to the investigation of structure, dynamics and chemical reaction dynamics is discussed. Specifically, the particle exchange, diffusion and reorientational dynamics in the electrochemical double layer is analyzed in some detail. Some recent developments concerning the simulation of the dynamics of electron
Molecular Dynamic Simulations of Interaction of an AFM Probe with the Surface of an SCN Sample
NASA Technical Reports Server (NTRS)
Bune, Adris; Kaukler, William; Rose, M. Franklin (Technical Monitor)
2001-01-01
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.
Dynamics, flexibility, and allostery in molecular chaperonins.
Skjærven, Lars; Cuellar, Jorge; Martinez, Aurora; Valpuesta, José María
2015-09-14
The chaperonins are a family of molecular chaperones present in all three kingdoms of life. They are classified into Group I and Group II. Group I consists of the bacterial variants (GroEL) and the eukaryotic ones from mitochondria and chloroplasts (Hsp60), while Group II consists of the archaeal (thermosomes) and eukaryotic cytosolic variants (CCT or TRiC). Both groups assemble into a dual ring structure, with each ring providing a protective folding chamber for nascent and denatured proteins. Their functional cycle is powered by ATP binding and hydrolysis, which drives a series of structural rearrangements that enable encapsulation and subsequent release of the substrate protein. Chaperonins have elaborate allosteric mechanisms to regulate their functional cycle. Long-range negative cooperativity between the two rings ensures alternation of the folding chambers. Positive intra-ring cooperativity, which facilitates concerted conformational transitions within the protein subunits of one ring, has only been demonstrated for Group I chaperonins. In this review, we describe our present understanding of the underlying mechanisms and the structure-function relationships in these complex protein systems with a particular focus on the structural dynamics, allostery, and associated conformational rearrangements. PMID:26140986
Molecular dynamics studies of lanthanum chloride solutions
Meier, W.; Bopp, Ph. (Institut fuer Physikalische Chemie, Aachen (West Germany)); Probst, M.M. (Universitaet Innsbruck (Austria)); Spohr, E. (Univ. of California, Irvine (USA)); Lin, J.L. (Boston College, Chestnut Hill, MA (USA))
1990-05-31
Molecular dynamics studies are reported for LaCl{sub 3} solutions at two different concentrations and temperatures, and for isolated aqueous La{sup 3+} ions. Ion-water clusters La(H{sub 2}O){sub n}{sup 3+} with n = 61 and n = 100 and systems consisting of one ion and 100 or 200 water molecules in the usual periodic box, as well as solutions of 7 (4) cations and 21 (12) anions in 190 (200) water molecules, corresponding to 2 and 1.1 m solutions, respectively, were investigated. The 2 m solution was investigated at two different temperatures. The results for the static structure, with special emphasis on the hydration structure of the La{sup 3+} ion, are discussed in terms of radial distribution functions and resulting hydration numbers, and various other correlations. These results are compared with X-ray data and discussed in light of the hydration numbers observed for aqueous ions in general.
Molecular Dynamics Study of Helicobacter pylori Urease.
Minkara, Mona S; Ucisik, Melek N; Weaver, Michael N; Merz, Kenneth M
2014-05-13
Helicobacter pylori have been implicated in an array of gastrointestinal disorders including, but not limited to, gastric and duodenal ulcers and adenocarcinoma. This bacterium utilizes an enzyme, urease, to produce copious amounts of ammonia through urea hydrolysis in order to survive the harsh acidic conditions of the stomach. Molecular dynamics (MD) studies on the H. pylori urease enzyme have been employed in order to study structural features of this enzyme that may shed light on the hydrolysis mechanism. A total of 400 ns of MD simulation time were collected and analyzed in this study. A wide-open flap state previously observed in MD simulations on Klebsiella aerogenes [Roberts et al. J. Am. Chem. Soc. 2012, 134, 9934] urease has been identified in the H. pylori enzyme that has yet to be experimentally observed. Critical distances between residues on the flap, contact points in the closed state, and the separation between the active site Ni(2+) ions and the critical histidine ?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
Molecular Dynamics Study of Helicobacter pylori Urease
2015-01-01
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 Ni2+ 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
NASA Astrophysics Data System (ADS)
Calero, S.; Lago, S.; Garzón, B.
1999-09-01
Molecular dynamics simulations varying the molecular mass distribution in linear molecules are performed to search for a direct test of Hubbard relations for liquid state dynamics. Results are obtained for series of models with different moments of inertia and the same multipoles and molecular length. The intermolecular potential is composed of different contributions including a nonpolar term. This potential allows for a steady variation of moment of inertia. Correlation times are directly checked with Hubbard relations and a nearly quantitative agreement found. Nonpreviously reported relationships between single correlation times and transport coefficients versus molecular moment of inertia are shown.
Multiscale molecular dynamics using the matched interface and boundary method
Geng Weihua [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Wei, G.W., E-mail: wei@math.msu.ed [Department of Mathematics, Michigan State University, East Lansing, MI 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI 48824 (United States)
2011-01-20
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.
High-order harmonic spectroscopy of molecular structure and dynamics
NASA Astrophysics Data System (ADS)
Zhou, Xibin
The recent developments of high repetition rate and high average power ultrafast laser open the door for probing molecular structure and dynamics with intense laser fields. In this regime, the electric field of the laser is comparable to the binding field of the electron in the outer valence shell of atoms or molecules. Thus the potential is strongly modified by the laser electric field as compared to field-free atomic or molecular potential, and the probability for ionization is dramatically enhanced. High harmonic generation (HHG), as an ionization-initiated strong field process, can be explained well by the semiclassical recollision model. In this work, we demonstrate HHG as a new spectroscopic method for determining the molecular structure of simple linear molecules (such as N2 and CO2), and for monitoring the real-time molecular dynamics of polyatomic molecules (such as N2O4). First, we use an extreme-ultraviolet interferometry to measure the phase of high-order harmonic generation from transiently aligned CO2 molecules. We unambiguously observe a reversal in phase of the high order harmonic emission for higher harmonic orders with a sufficient degree of alignment. This results from molecular-scale quantum interferences between the molecular electronic wave function and the re-colliding electron as it recombines with the molecule, and it is consistent with a plane wave model. We also perform similar experiments with N2 molecules and observe behaviors that can not be predicted by the plane-wave model. Second, we perform an accurate polarimetry measurement of high harmonic emission from aligned molecules. Surprisingly, we find that harmonic emission from N2 molecules can be strongly elliptically polarized even when driven by linearly polarized laser fields. We extract the phase difference between the parallel and perpendicular components of the high harmonic field, which strongly depends on the harmonic order. This nontrivial phase indicates a breakdown of plane wave approximation. This work also shows that it is possible to engineer the polarization properties of harmonic emission by carefully preparing a molecular medium. Finally, we show that high harmonic emission can reveal coupled electronic and nuclear dynamics in polyatomic molecules. By exciting large amplitude and relative slow vibrations in the N2O4 molecule, we show that tunnel ionization accesses the ground state of the ion at the outer turning point of the vibration, whereas the first excited state is populated at the inner turning point of the vibration motion. This state switching due to the coupled electronic and nuclear motions is manifested as bright bursts of high harmonic light that are emitted mostly at the outer turning point of the vibration, due to the different symmetries of the ground state and the first excited state of the cation.
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica
NASA Astrophysics Data System (ADS)
Hamdan, Rashid; Trinastic, Jonathan P.; Cheng, H. P.
2014-08-01
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.
Molecular dynamics study of the mechanical loss in amorphous pure and doped silica.
Hamdan, Rashid; Trinastic, Jonathan P; Cheng, H P
2014-08-01
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. PMID:25106591
Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.
M'Koma, Amosy E
2014-11-27
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
Zoonotic Potential and Molecular Epidemiology of Giardia Species and Giardiasis†
Feng, Yaoyu; Xiao, Lihua
2011-01-01
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
Masses, luminosities and dynamics of galactic molecular clouds
NASA Technical Reports Server (NTRS)
Solomon, P. M.; Rivolo, A. R.; Mooney, T. J.; Barrett, J. W.; Sage, L. J.
1987-01-01
Star formation in galaxies takes place in molecular clouds and the Milky Way is the only galaxy in which it is possible to resolve and study the physical properties and star formation activity of individual clouds. The masses, luminosities, dynamics, and distribution of molecular clouds, primarily giant molecular clouds in the Milky Way are described and analyzed. The observational data sets are the Massachusetts-Stony Brook CO Galactic Plane Survey and the IRAS far IR images. The molecular mass and infrared luminosities of glactic clouds are then compared with the molecular mass and infrared luminosities of external galaxies.
Gedeon, Patrick C; Thomas, James R; Madura, Jeffry D
2015-01-01
Molecular dynamics simulation provides a powerful and accurate method to model protein conformational change, yet timescale limitations often prevent direct assessment of the kinetic properties of interest. A large number of molecular dynamic steps are necessary for rare events to occur, which allow a system to overcome energy barriers and conformationally transition from one potential energy minimum to another. For many proteins, the energy landscape is further complicated by a multitude of potential energy wells, each separated by high free-energy barriers and each potentially representative of a functionally important protein conformation. To overcome these obstacles, accelerated molecular dynamics utilizes a robust bias potential function to simulate the transition between different potential energy minima. This straightforward approach more efficiently samples conformational space in comparison to classical molecular dynamics simulation, does not require advanced knowledge of the potential energy landscape and converges to the proper canonical distribution. Here, we review the theory behind accelerated molecular dynamics and discuss the approach in the context of modeling protein conformational change. As a practical example, we provide a detailed, step-by-step explanation of how to perform an accelerated molecular dynamics simulation using a model neurotransmitter transporter embedded in a lipid cell membrane. Changes in protein conformation of relevance to the substrate transport cycle are then examined using principle component analysis. PMID:25330967
Relationship between nanocrystalline and amorphous microstructures by molecular dynamics simulation
Keblinski, P.; Phillpot, S.R.; Wolf, D. [Argonne National Lab., IL (United States); Gleiter, H. [Forschungszentrum Karlsruhe GmbH Technik und Umwelt (Germany)
1996-08-01
A recent molecular dynamics simulation method for growth of fully dense nanocrystalline materials crystallized from melt was used with the Stillinger-Weber three-body potential to synthesize nanocrystalline Si with a grain size up to 75{Angstrom}. Structures of the highly constrained grain boundaries (GBs), triple lines, and point grain junctions were found to be highly disordered and similar to the structure of amorphous Si. These and earlier results for fcc metals suggest that a nanocrystalline microstructure may be viewed as a two-phase system, namely an ordered crystalline phase in the grain interiors connected by an amorphous, intergranular, glue-like phase. Analysis of the structures of bicrystalline GBs in the same materials reveals the presence of an amorphous intergranular equilibrium phase only in the high-energy but not the low-energy GBs, suggesting that only high-energy boundaries are present in nanocrystalline microstructures.
Molecular Dynamics Simulations of Carbon Nanotubes in Water
NASA Technical Reports Server (NTRS)
Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.
2000-01-01
We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.
Molecular Dynamics Simulations of Temperature Equilibration in Dense Hydrogen
Glosli, J; Graziani, F; More, R; Murillo, M; Streitz, F; Surh, M; Benedict, L; Hau-Riege, S; Langdon, A; London, R
2008-02-14
The temperature equilibration rate in dense hydrogen (for both T{sub i} > T{sub e} and T{sub i} < T{sub e}) has been calculated with large-scale molecular dynamics simulations for temperatures between 10 and 300 eV and densities between 10{sup 20}/cc to 10{sup 24}/cc. Careful attention has been devoted to convergence of the simulations, including the role of semiclassical potentials. We find that for Coulomb logarithms L {approx}> 1, Brown-Preston-Singleton [Brown et al., Phys. Rep. 410, 237 (2005)] with the sub-leading corrections and the fit of Gericke-Murillo-Schlanges [Gericke et al., PRE 65, 036418 (2003)] to the T-matrix evaluation of the collision operator, agrees with the MD data to within the error bars of the simulation. For more strongly-coupled plasmas where L {approx}< 1, our numerical results are consistent with the fit of Gericke-Murillo-Schlanges.
Structure of Hexafluoroisopropanol-Water Mixtures by Molecular Dynamics Simulations
NASA Astrophysics Data System (ADS)
Yamaguchi, Toshio; Imura, Shinya; Kai, Tadashi; Yoshida, Koji
2013-02-01
The structure of aqueous mixtures of 1,1,1,3,3,3-hexafluoro-propane-2-ol (HFIP) has been investigated at an alcohol mole fraction (xHFIP) of 0.1, 0.2, and 0.4 by molecular dynamics (MD) simulation. The simulated pair correlation functions were compared with those obtained by empirical potential structure refinement (EPSR) modelling combined with neutron diffraction with isotopic substitution experiment. It is demonstrated that microheterogeneities of HFIP and water clusters occur at xHFIP = 0.1 and 0.2 and that the tetrahedral-like structure of water is mostly disrupted at xHFIP = 0.4. The evolution of the microscopic structure of the water-water, alcohol-water, and alcohol-alcohol pairs with alcohol concentration is revealed in terms of pair correlation functions and discussed from the standpoint of hydrophilic and hydrophobic hydration.
A molecular dynamics study of a steric multipole model of liquid crystal molecular geometry
NASA Astrophysics Data System (ADS)
Neal, M. P.; Parker, A. J.; Care, C. M.
We report results from a series of molecular dynamics simulations designed to study the phase behaviour of model rod-like liquid crystal molecules with different geometries interacting via the Gay-Berne potential. Following the classification of molecular geometry in terms of a multipole expansion in steric asymmetry, two models have been studied in detail: a zigzag model defined as a steric quadrupole and a triangle model defined as a longitudinal steric dipole, and comparison has been made with a cylindrical model. Results from the NVE ensemble indicate that the model steric quadrupole delays the temperature of onset of the nematic phase. Extensive simulations in the NPT ensemble demonstrate a similar trend in the temperature of onset of the smectic B phase, with a lower temperature of onset observed with the steric quadrupole than the steric dipole. Local antiparallel steric ordering within a layer was observed with the model steric dipole in the crystal B phase but not with the model steric quadrupole. This structure is in agreement with experimental results and with the prediction of the generalized molecular asymmetry model. The steric quadrupole demonstrated a rippled structure through the smectic B phase, increasing in amplitude and wavelength sufficiently to tilt molecules along a wave with respect to the system director as the system was cooled. This structure was almost absent in the final crystal structure simulated. The ensemble also allowed comparison with experiment and agreement, scaled with respect to the single-site Gay-Berne mesogen, was found to be good.
Bohm's Quantum Potential and the Visualization of Molecular Structure
NASA Technical Reports Server (NTRS)
Levit, Creon; Chancellor, Marisa K. (Technical Monitor)
1997-01-01
David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
NASA Astrophysics Data System (ADS)
Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-01
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions. PMID:25106573
Surface Diffusion of Single Polymer Chain Using Molecular Dynamics SIMULATION*
NASA Astrophysics Data System (ADS)
Desai, Tapan; Keblinski, Pawel; Kumar, Sanat; Granick, Steve
2004-05-01
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.
Dynamic behavioural interpretation of cervical intraepithelial neoplasia with molecular biomarkers
Baak, J P A; Kruse, A?J; Robboy, S J; Janssen, E A M; van Diermen, B; Skaland, I
2006-01-01
The microscopic phenotype of cervical intraepithelial neoplasia (CIN) reflects a fine balance between factors that promote or reduce CIN development. A shortcoming of the current grading system is its reliance on static morphology and microscopic haematoxylin–eosin features of the epithelium alone. In reality, CIN is a dynamic process, and the epithelium may exhibit differing results over time. Functional biomarkers p16, Ki?67, p53, retinoblastoma protein cytokeratin (CK)14 and CK13, help in the assessment of an individual CIN's lesion's potential for progression and regression. The aggregate information provided by these biomarkers exceeds the value of the classic grading system. Consequently, many more CINs that will either regress or progress can be accurately identified. These findings agree with known molecular interactions between HPV and the host. For accurate interpretation of a CIN, it is essential that these biomarkers be determined quantitatively and separately in the superficial, middle and deep layers of the epithelium. Such geography?specific epithelial evaluations of quantitative biomarkers emphasise the dynamic nature of a particular CIN lesion, thereby changing the art of static morphology grading into dynamic interpretation of the diseased tissue, with a strong prognostic effect. PMID:16679355
Molecular dynamics simulations of displacement cascades in GaAs.
Foiles, Stephen Martin
2010-04-01
The quantification of the production of primary defects via displacement cascades is an important ingredient in the prediction of the influence of radiation on the performance of electronic components in radiation environments. Molecular dynamics simulations of displacement cascades are performed for GaAs The interatomic interactions are described using a recently proposed Bond Order Potential, and a simple model of electronic stopping is incorporated. The production of point defects is quantified as a function of recoil energy and recoil species. Correlations in the point defects are examined. There are a large number of anti-site defects nearest-neighbor pairs as well as di-vacancies and larger order vacancy clusters. Radiation damage and ion implantation in materials have been studied via molecular dynamics for many years. A significant challenge in these simulations is the detailed identification and quantification of the primary defect production. For the present case of a compound semiconductor, GaAs, there are a larger number of possible point defects compared to elemental materials; two types of vacancies, two types of interstitials and antisite defects. This is further complicated by the fact that, in addition to the formation of point defects, amorphous zones may also be created. The goal of the current work is to quantify the production of primary defects in GaAs due to radiation exposures. This information will be used as part of an effort to predict the influence of radiation environments on the performance of electronic components and circuits. The data provide the initial state for continuum-level analysis of the temporal evolution of defect populations. For this initial state, it is important to know both the number of the various point defects that may be produced as well as the initial spatial correlations between the primary defects. The molecular dynamics simulations employ a recently developed Bond Order Potential (BOP) for GaAs. The analysis of the resulting atomic configurations follows a generalization of methods presented previously for elemental Si. The number of point defects of various types, exclusive of the amorphous zones, is predicted as a function of recoil energy. It is also shown that certain primary point defects are initially formed in binary or larger clusters.
Direct Molecular Dynamics Observation of Protein Folding Transition State Ensemble
Stanley, H. Eugene
interests in the past decade (Li and Daggett, 1994,1998; Munoz and Eaton, 1999; Galzitskaya and Finkelstein). Temperature-induced unfolding (Li and Daggett, 1994,1998) in all-atom molecular dynamics simulations
RPMDrate: Bimolecular chemical reaction rates from ring polymer molecular dynamics
Suleimanov, Yu.V.
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 ...
Molecular Dynamics Simulation of Homogeneous Crystal Nucleation in Polyethylene
Yi, Peng
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 ...
Molecular dynamics for full QCD simulations with an improved action
Xiang-Qian Luo
2004-03-27
I derive the equation of motion in molecular dynamics for doing full lattice QCD simulations with clover quarks. The even-odd preconditioning technique, expected to significantly reduce the computational effort, is further developed for the simulations.
CHARACTERIZING COUPLED CHARGE TRANSPORT WITH MULTISCALE MOLECULAR DYNAMICS
Swanson, Jessica
2011-08-31
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.
Framework Design, Parallelization and Force Computation in Molecular Dynamics
Izaguirre, Jesús A.
Framework Design, Parallelization and Force Computation in Molecular Dynamics Thierry Matthey conditions . . . . . . . . . . . . . . . . . . . . . . . . 12 3 Force Computation 13 3.1 Fast electrostatic force algorithms . . . . . . . . . . . . . . . . . 14 3.2 Standard Ewald summation
Can Dynamic Contact Angle Be Measured Using Molecular Modeling?
Malani, Ateeque A. A. G.
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 ...
Nonadiabatic Molecular Dynamics and Orthogonality Constrained Density Functional Theory
NASA Astrophysics Data System (ADS)
Shushkov, Philip Georgiev
The exact quantum dynamics of realistic, multidimensional systems remains a formidable computational challenge. In many chemical processes, however, quantum effects such as tunneling, zero-point energy quantization, and nonadiabatic transitions play an important role. Therefore, approximate approaches that improve on the classical mechanical framework are of special practical interest. We propose a novel ring polymer surface hopping method for the calculation of chemical rate constants. The method blends two approaches, namely ring polymer molecular dynamics that accounts for tunneling and zero-point energy quantization, and surface hopping that incorporates nonadiabatic transitions. We test the method against exact quantum mechanical calculations for a one-dimensional, two-state model system. The method reproduces quite accurately the tunneling contribution to the rate and the distribution of reactants between the electronic states for this model system. Semiclassical instanton theory, an approach related to ring polymer molecular dynamics, accounts for tunneling by the use of periodic classical trajectories on the inverted potential energy surface. We study a model of electron transfer in solution, a chemical process where nonadiabatic events are prominent. By representing the tunneling electron with a ring polymer, we derive Marcus theory of electron transfer from semiclassical instanton theory after a careful analysis of the tunneling mode. We demonstrate that semiclassical instanton theory can recover the limit of Fermi's Golden Rule rate in a low-temperature, deep-tunneling regime. Mixed quantum-classical dynamics treats a few important degrees of freedom quantum mechanically, while classical mechanics describes affordably the rest of the system. But the interface of quantum and classical description is a challenging theoretical problem, especially for low-energy chemical processes. We therefore focus on the semiclassical limit of the coupled nuclear-electronic dynamics. We show that the time-dependent Schrodinger equation for the electrons employed in the widely used fewest switches surface hopping method is applicable only in the limit of nearly identical classical trajectories on the different potential energy surfaces. We propose a short-time decoupling algorithm that restricts the use of the Schrodinger equation only to the interaction regions. We test the short-time approximation on three model systems against exact quantum-mechanical calculations. The approximation improves the performance of the surface hopping approach. Nonadiabatic molecular dynamics simulations require the efficient and accurate computation of ground and excited state potential energy surfaces. Unlike the ground state calculations where standard methods exist, the computation of excited state properties is a challenging task. We employ time-independent density functional theory, in which the excited state energy is represented as a functional of the total density. We suggest an adiabatic-like approximation that simplifies the excited state exchange-correlation functional. We also derive a set of minimal conditions to impose exactly the orthogonality of the excited state Kohn-Sham determinant to the ground state determinant. This leads to an efficient, variational algorithm for the self-consistent optimization of the excited state energy. Finally, we assess the quality of the excitation energies obtained by the new method on a set of 28 organic molecules. The new approach provides results of similar accuracy to time-dependent density functional theory.
Special issue on ultrafast electron and molecular dynamics
NASA Astrophysics Data System (ADS)
Hishikawa, Akiyoshi; Martin, Fernando; Vrakking, Marc
2013-07-01
Your invitation to submit. Journal of Physics. B: Atomic Molecular and Optical Physics (JPhysB) is delighted to announce a forthcoming special issue on ultrafast electron and molecular dynamics to appear in 2014, and invites you to submit a paper. Within the last decade, a number of novel approaches have emerged, both experimental and theoretical, that allow the investigation of (time-resolved) molecular dynamics in novel ways not anticipated before. Experimentally, the introduction of novel light sources such as high-harmonic generation and XUV/x-ray free electron lasers, and the emergence of novel detection strategies, such as time-resolved electron/x-ray diffraction and the fully coincident detection of electrons and fragment ions in reaction microscopes, has significantly expanded the arsenal of available techniques, and has taken studies of molecular dynamics into new domains of spectroscopic, spatial and temporal resolution, the latter including first explorations into the attosecond domain. Along the way, particular types of molecular dynamics, such as dynamics around conical intersections, have gained an increased prominence, sparked by an emerging realization about the essential role that this dynamics plays in relaxation pathways in important bio-molecular systems. The progress on the theoretical side has been no less impressive. Novel generations of supercomputers and a series of novel computational strategies have allowed nearly exact calculations in small molecules, as well as highly successful approximate calculations in large, polyatomic molecules. Frequent and intensive collaborations involving both theory and experiment have been essential for the progress that has been accomplished. The special issue 'Ultrafast electron and molecular dynamics' seeks to provide an overview of some of the most important developments in the field, while at the same time indicating how studies of (time-resolved) molecular dynamics are likely to evolve in the coming years. You are invited to submit your article by 1 December 2013.
NASA Astrophysics Data System (ADS)
Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B.
2015-06-01
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T? ˜ 315 ± 5 K, was spotted at T? ˜ 283 K and T? ˜ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two crossovers at molecular level are discussed.
Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B
2015-06-28
In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(?) ? 315 ± 5 K, was spotted at T(?) ? 283 K and T(?) ? 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two crossovers at molecular level are discussed. PMID:26133441
Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories
Caflisch, Amedeo
Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories Andreas Vitalis Zurich, Switzerland *S Supporting Information ABSTRACT: The coarse-graining of data from molecular. In this contribution, we present a tree-based algorithm to partition conformations of biomolecules into sets of similar
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...
Protein dynamics and the immunological evolution of molecular recognition
Yin, Jun
Protein dynamics and the immunological evolution of molecular recognition Ralph Jimenez , Georgina for review September 8, 2003) While it is accepted that protein flexibility plays a role in protein folding, catalysis, and molecular recognition, few techniques are capable of the rigorous measurement of protein
A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics
Chowdhury, Rezaul A.
of important molecular prop- erties (e.g., surface area, volume, polarization energy, etc.) that are needed for computing binding affinities in drug de- sign or in molecular dynamics calculations. DPG can addi- tionally is granted without fee provided that copies are not made or distributed for profit or commercial advantage
A Dynamic Data Structure for Flexible Molecular Maintenance and Informatics #
Chowdhury, Rezaul A.
of important molecular prop erties (e.g., surface area, volume, polarization energy, etc.) that are needed for computing binding a#nities in drug de sign or in molecular dynamics calculations. DPG can addi tionally or commercial advantage and that copies bear this notice and the full citation on the first page. To copy
Iyengar, Srinivasan S.
change in topography of the potential energy surface at finite temperature, dominate important structural bonded systems such as water clusters. The areas that are covered in this article include the field of ab using ab initio molecular dynamics in conjunction with quantum wavepackets Srinivasan S. Iyengar
J. Phys. Chem. 1903, 87, 4277-4201 4277 Molecular Dynamics Study of Ice Crystallite Melting
Stillinger, Frank
J. Phys. Chem. 1903, 87, 4277-4201 4277 Molecular Dynamics Study of Ice Crystallite Melting Thomas been used to examine the melting process for a 250-moleculeice Ih crystallite. The ST2 potential on those interactions. Melting was observed to begin at the crystallite surface and to proceed inward
Noble gas temperature control of metal clusters: A molecular dynamics study
Tománek, David
Noble gas temperature control of metal clusters: A molecular dynamics study Jan Westergren temperature, iv gasmetal interaction strength, v metal potential, and vi noble gas mass. With these results, calculating classical tra- jectories of collisions between noble gas atoms and metal clusters
Mg2SiO4 liquid under high pressure from molecular dynamics Omar Adjaoud a
Steinle-Neumann, Gerd
the sinking velocity of a solid sphere through a liquid can be related to viscosity by Stokes' law (Kushiro Thermodynamics Diffusivity Viscosity We use a flexible potential model to perform large-scale molecular dynamics pressure. At high pressure viscosity is measured most directly by the "falling sphere" method, in which
Solubility of KF in water by molecular dynamics using the Kirkwood integration method
Mauro Ferrario; Giovanni Ciccotti; Eckhard Spohr; Thierry Cartailler; Pierre Turq
2002-01-01
We have studied the solubility of potassium fluoride in aqueous solution at near ambient condition, using a simple modeling for the ion and water interactions and computing the values of the chemical potential by molecular dynamics within the framework of Kirkwood generalized thermodynamic integration approach for the evaluation of free energy differences. We report the details of the procedure we
Molecular dynamics simulation of the contact angle of liquids on solid surfaces
Zhigilei, Leonid V.
Molecular dynamics simulation of the contact angle of liquids on solid surfaces Bo Shi and Vijay K of Physics. DOI: 10.1063/1.3055600 I. INTRODUCTION Solid-liquid-vapor interaction phenomena have an im argon and a virtual solid wall. He modeled the solid-liquid interaction by a 9,3 potential and assumed
Ole Kr. Forrisdahl
1996-01-01
The melting of structure I methane clathrate hydrate has been investigated using NVT molecular dynamics simulations, for a number of potential energy models for water and methane. The equilibrated hydrate crystal has been heated carefully from 270 K, in steps of 5 K, until a well defined phase instability appears. At a density of 0s92 g cm-3, an upper bound
NASA Astrophysics Data System (ADS)
Niklasson, Anders; Cawkwell, Marc
2012-02-01
Born-Oppenheimer molecular dynamics (BOMD) based on density functional theory offers a very accurate quantum mechanical approach to atomistic simulations that is more reliable and general compared to classical MD. Unfortunately, BOMD simulations are often limited by a high computational cost or by problems such as unbalanced phase space trajectories, numerical instabilities and a systematic long-term energy drift. These problems become particularly severe in combination with reduced complexity or linear scaling algorithms that are necessary for the study of large systems. We have recently taken some steps toward a new generation of first principles MD, which combines some of the best features of regular BOMD and Car-Parrinello MD, while avoiding their most serious shortcomings. The new dynamics is given in terms of an extended Lagrangian (XL), where auxiliary extended electronic degrees of freedom are added to the nuclear part. Our framework enables accurate geometric integration of both the nuclear and electronic degrees of freedom that provide a time-reversible and energy conserving dynamics on the ground state BO potential energy surface that is stable also under approximate SCF convergence. XL-BOMD provides a surprisingly simple and general framework for atomistic simulations
Wood, Mitchell A; van Duin, Adri C T; Strachan, Alejandro
2014-02-01
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
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Yoo, Jejoong; Aksimentiev, Aleksei
2013-01-01
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects. PMID:24277840
Molecular Dynamics in Self-Assembled Monolayers
Jason Bochinski; Derrick Stevens; Mary Scott; Laura Guy; Casey Dedeugd; Laura Clarke
2007-01-01
Silane self-assembled monolayers (SAMs) are an important tool for both scientific research and technological applications. Despite their widespread use, few experimental investigations have addressed molecular motion within these films, which offer a unique and useful physical system for fundamental scientific studies, such as observing dipolar and other glass transitions in two-dimensions. In addition, relaxations such as ``rotator'' phases where molecular
Phonon properties of graphene derived from molecular dynamics simulations.
Koukaras, Emmanuel N; Kalosakas, George; Galiotis, Costas; Papagelis, Konstantinos
2015-01-01
A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the overall phonon dispersion, using available inelastic x-ray scattering data. The method is promising for systems with large scale periodicity, accounts for anharmonic effects and non-bonding interactions with a general environment, and it is applicable under finite temperatures. The temperature dependence of the phonon dispersion curves has been examined with emphasis on the doubly degenerate Raman active ?-E2g phonon at the zone centre, where experimental results are available. The potentials used show diverse behaviour. The Tersoff-2010 potential exhibits the most systematic and physically sound behaviour in this regard, and gives a first-order temperature coefficient of ??=?-0.05?cm(-1)/K for the ?-E2g shift in agreement with reported experimental values. PMID:26316252
Phonon properties of graphene derived from molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Koukaras, Emmanuel N.; Kalosakas, George; Galiotis, Costas; Papagelis, Konstantinos
2015-08-01
A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the overall phonon dispersion, using available inelastic x-ray scattering data. The method is promising for systems with large scale periodicity, accounts for anharmonic effects and non-bonding interactions with a general environment, and it is applicable under finite temperatures. The temperature dependence of the phonon dispersion curves has been examined with emphasis on the doubly degenerate Raman active ?-E2g phonon at the zone centre, where experimental results are available. The potentials used show diverse behaviour. The Tersoff-2010 potential exhibits the most systematic and physically sound behaviour in this regard, and gives a first-order temperature coefficient of ??=??0.05?cm?1/K for the ?-E2g shift in agreement with reported experimental values.
Phonon properties of graphene derived from molecular dynamics simulations
Koukaras, Emmanuel N.; Kalosakas, George; Galiotis, Costas; Papagelis, Konstantinos
2015-01-01
A method that utilises atomic trajectories and velocities from molecular dynamics simulations has been suitably adapted and employed for the implicit calculation of the phonon dispersion curves of graphene. Classical potentials widely used in the literature were employed. Their performance was assessed for each individual phonon branch and the overall phonon dispersion, using available inelastic x-ray scattering data. The method is promising for systems with large scale periodicity, accounts for anharmonic effects and non-bonding interactions with a general environment, and it is applicable under finite temperatures. The temperature dependence of the phonon dispersion curves has been examined with emphasis on the doubly degenerate Raman active ?-E2g phonon at the zone centre, where experimental results are available. The potentials used show diverse behaviour. The Tersoff-2010 potential exhibits the most systematic and physically sound behaviour in this regard, and gives a first-order temperature coefficient of ??=??0.05?cm?1/K for the ?-E2g shift in agreement with reported experimental values. PMID:26316252
Mixtures of protic ionic liquids and molecular cosolvents: A molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Docampo-Álvarez, Borja; Gómez-González, Víctor; Méndez-Morales, Trinidad; Carrete, Jesús; Rodríguez, Julio R.; Cabeza, Óscar; Gallego, Luis J.; Varela, Luis M.
2014-06-01
In this work, the effect of molecular cosolvents (water, ethanol, and methanol) on the structure of mixtures of these compounds with a protic ionic liquid (ethylammonium nitrate) is analyzed by means of classical molecular dynamics simulations. Included are as-yet-unreported measurements of the densities of these mixtures, used to test our parameterized potential. The evolution of the structure of the mixtures throughout the concentration range is reported by means of the calculation of coordination numbers and the fraction of hydrogen bonds in the system, together with radial and spatial distribution functions for the various molecular species and molecular ions in the mixture. The overall picture indicates a homogeneous mixing process of added cosolvent molecules, which progressively accommodate themselves in the network of hydrogen bonds of the protic ionic liquid, contrarily to what has been reported for their aprotic counterparts. Moreover, no water clustering similar to that in aprotic mixtures is detected in protic aqueous mixtures, but a somehow abrupt replacing of [NO3]- anions in the first hydration shell of the polar heads of the ionic liquid cations is registered around 60% water molar concentration. The spatial distribution functions of water and alcohols differ in the coordination type, since water coordinates with [NO3]- in a bidentate fashion in the equatorial plane of the anion, while alcohols do it in a monodentate fashion, competing for the oxygen atoms of the anion. Finally, the collision times of the different cosolvent molecules are also reported by calculating their velocity autocorrelation functions, and a caging effect is observed for water molecules but not in alcohol mixtures.
Chu, Shih-I; Yao, Guanhua
1993-07-01
We extend our previous study [Chem. Phys. Lett. 197, 413 (1992)] of the molecular stabilization in intense laser fields by considering the dynamical behavior of the H+2 molecules in intense femtosecond short laser pulses at 775 nm. Significant...
The Art of Molecular Dynamics Simulation (by D. C. Rapaport)
NASA Astrophysics Data System (ADS)
Molner, Stephen P.
1999-02-01
Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95. This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a complete program listing or a series of modifications or additions to a program from an earlier case study. The initial conditions of the model, organization of the input and output, accuracy, convergence, and efficiency are also addressed for each case and, of course, the results of the computation are given and discussed. The book begins with the simplest case of basic molecular dynamics, a sift-disk fluid. The development is discussed in considerable depth to set the tone of the work. Later chapters extend the basic model in various directions, deal with various types of measurements, improve the computational methods, and introduce new models for more complex problems. These chapters also discuss the methodology for simulating monatomic systems and focus on measuring the thermodynamic and structural properties of systems in equilibrium. Consideration is given to the dynamical properties of equilibrium systems, including transport coefficients and the correlation functions that characterize space- and time-dependent properties. Chapters are devoted to the study of systems under constant temperature and pressure and the dynamics of rigid systems. It is difficult to cover all aspects of such a broad topic as the subject of this book; and the author has not attempted an exhaustive or encyclopedic coverage, but has produced an excellent introduction to the subject. The publisher has made the implementation of the numerous programs essentially painless by making them available via browser and the World Wide Web. The easy availability of the software, written in C, was welcomed by this old Fortran programmer. It is to be hoped that this service is representative of a trend in technical publishing. Overall this work is a pleasure to read and study and would be a valuable addition to the library of both the beginner and the experienced practitioner of the art.
Westhof, Eric
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
Ghosh, Soumadwip; Chakrabarti, Rajarshi
2015-01-01
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in human body, affect the thermodynamic stability of the duplex DNA and exhibit preferential binding. Here, using atomistic molecular dynamics simulations we investigate the preferential binding of metal ion such as Na+ and molecular ions such as tetramethyl ammonium (TMA+) and 2-hydroxy-N,N,N-trimethylethanaminium (CHO+) to double stranded DNA. The thermodynamic driving force for a particular molecular ion- DNA interaction is determined by decomposing the free energy of binding into its entropic and enthalpic contributions. Our simulations show that each of these molecular ions preferentially binds to the minor groove of the DNA and the extent of binding is highest for CHO+. The ion binding processes are found to be entropically favourable. In addition, the contribution of hy...
Transient Dynamics in Molecular Junctions: Coherent Bichromophoric Molecular Electron Pumps
Roie Volkovich; Uri Peskin
2010-01-01
The possibility of using single molecule junctions as electron pumps for\\u000aenergy conversion and storage is considered. It is argued that the small\\u000adimensions of these systems enable to make use of unique intra-molecular\\u000aquantum coherences in order to pump electrons between two leads and to overcome\\u000arelaxation processes which tend to suppress the pumping efficiency. In\\u000aparticular, we demonstrate
Molecular dynamics simulation of poly(ethylene terephthalate) oligomers.
Wang, Qifei; Keffer, David J; Petrovan, Simioan; Thomas, J Brock
2010-01-21
Molecular dynamics simulations of poly(ethylene terephthalate) (PET) oligomers are performed in the isobaric-isothermal (NpT) ensemble at a state point typical of a finishing reactor. The oligomer size ranges from 1 to 10 repeat units. We report thermodynamic properties (density, potential energy, enthalpy, heat capacity, isothermal compressibility, and thermal expansivity), transport properties (self-diffusivity, zero-shear-rate viscosity, thermal conductivity), and structural properties (pair correlation functions, hydrogen bonding network, chain radius of gyration, chain end-to-end distance) as a function of oligomer size. We compare the results with existing molecular-level theories and experimental data. Scaling exponents as a function of degree of polymerization are extracted. The distribution of the end-to-end distance is bimodal for the dimer and gradually shifts to a single peak as the degree of polymerization increases. The scaling exponents for the average chain radius of gyration and end-to-end distance are 0.594 and 0.571, respectively. The values of the heat capacity, isothermal compressibility, and thermal expansivity agree well with the available experimental data, which are of much longer PET chains. The scaling exponents for the self-diffusivity and zero-shear-rate viscosity are, respectively, -2.01 and 0.96, with the latter one being close to the theoretical prediction 1.0 for short-chain polymers. PMID:20017524
Molecular dynamics of the water liquid-vapor interface
NASA Technical Reports Server (NTRS)
Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)
1987-01-01
The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.
Molecular dynamics simulation of pervaporation in zeolite membranes
NASA Astrophysics Data System (ADS)
Jia, W.; Murad, S.
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.
Fracture of nanophase ceramics: A molecular-dynamics study
Nakano, Aiichiro; Kalia, R.K.; Omeltchenko, A.; Tsuruta, K.; Vashishta, P. [Louisiana State Univ., Baton Rouge, LA (United States)
1997-09-01
New multiscale algorithms and a load-balancing scheme are combined for molecular-dynamics simulations of nanocluster-assembled ceramics on parallel computers. Million-atom simulations of the dynamic fracture in nanophase silicon nitride reveal anisotropic self-affine structures and crossover phenomena associated with fracture surfaces.
Nonequilibrium molecular dynamics simulation of a photoswitchable peptide
Phuong H. Nguyen; Gerhard Stock
2006-01-01
Femtosecond time-resolved experiments on photoswitchable peptides provide a new and promising way to study the folding and unfolding of biomolecules in real time and unprecedented detail. To obtain an appropriate theoretical description of these experiments, a computational strategy is presented that aims to extend well-established molecular dynamics simulation techniques to the description of photoinduced conformational dynamics in peptides. Adopting a
The Computer Simulation of Liquids by Molecular Dynamics.
ERIC Educational Resources Information Center
Smith, W.
1987-01-01
Proposes a mathematical computer model for the behavior of liquids using the classical dynamic principles of Sir Isaac Newton and the molecular dynamics method invented by other scientists. Concludes that other applications will be successful using supercomputers to go beyond simple Newtonian physics. (CW)
NASA Astrophysics Data System (ADS)
Wu, Bin
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
D. Sugny; Stéphane Vranckx; Mamadou Ndong; Nathalie Vaeck; Osman Atabek; Michèle Desouter-Lecomte
2014-12-15
The constraint of time-integrated zero-area on the laser field is a fundamental, both theoretical and experimental requirement in the control of molecular dynamics. By using techniques of local and optimal control theory, we show how to enforce this constraint on two benchmark control problems, namely molecular orientation and photofragmentation. The origin and the physical implications on the dynamics of this zero-area control field are discussed.
Thomas, David D.
Molecular Dynamics Simulation of Site-Directed Spin Labeling: Experimental Validation in Muscle, Molecular Biology, and Biophysics Department, University of Minnesota, Minneapolis, Minnesota 55455 USA ABSTRACT We have developed a computational molecular dynamics technique to simulate the motions of spin
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
Luchko, Tyler; Gusarov, Sergey; Roe, Daniel R.; Simmerling, Carlos; Case, David A.; Tuszynski, Jack; Kovalenko, Andriy
2010-01-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large 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
Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Tyler Luchko; C. Simmerling; S. Gusarov; D. R. Roe; David A. Case; Jack Tuszynski; Andriy Kovalenko
2010-01-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is
Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber
Luchko, T.; Simmerling, C.; Gusarov, S.; Roe, D.R., Case, D.A.; Tuszynski, J.; Kovalenko, A.
2010-02-01
We present the three-dimensional molecular theory of solvation (also known as 3D-RISM) coupled with molecular dynamics (MD) simulation by contracting solvent degrees of freedom, accelerated by extrapolating solvent-induced forces and applying them in large multiple time steps (up to 20 fs) to enable simulation of large biomolecules. The method has been implemented in the Amber molecular modeling package and is illustrated here on alanine-dipeptide and protein-G.
NASA Astrophysics Data System (ADS)
Grzybowski, A.; Paluch, M.; Grzybowska, K.; Haracz, S.
2010-10-01
In this communication, we provide a recipe for a consistent relation between dynamic scaling and thermodynamic properties well-grounded by the same intermolecular generalized Lennard-Jones potential, which is derived by using an essentially modified Avramov model within the framework of the "thermodynamic scaling" idea. This relation is experimentally verified very well for supercooled van der Waals liquids, and consequently, it can be a good basis for a proper universal description of molecular dynamics and thermodynamics of viscous systems.
Reactive Molecular Dynamics Simulations at the Petascale (Invited)
NASA Astrophysics Data System (ADS)
Nakano, A.
2013-12-01
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.
Molecular dynamics computer simulation of gas permeation in thin silicalite membranes
NASA Astrophysics Data System (ADS)
Pohl, Phillip I.
In this work we simulate the permeation of Lennard-Jones gases across a zeolite model membrane. Using a newly developed dual control volume grand canonical molecular dynamics technique, we create spatial variation in the chemical potential in a dynamical system and hence an accurate simulation of steady-state pressure-driven diffusion. The molecular sieving nature of microporous zeolites is discussed, and the results from the simulation are compared very favourably with recent experimentalresults of He, H2 and CH4 permeation through ZSM-5 polycrystalline membranes. A massively parallel algorithm is utilized to give a quick and insightful study of this and other microporous materials for use as membranes.
Dynamics of molecular superrotors in an external magnetic field
NASA Astrophysics Data System (ADS)
Korobenko, Aleksey; Milner, Valery
2015-08-01
We excite diatomic oxygen and nitrogen to high rotational states with an optical centrifuge and study their dynamics in an external magnetic field. Ion imaging is employed to directly visualize, and follow in time, the rotation plane of the molecular superrotors. The two different mechanisms of interaction between the magnetic field and the molecular angular momentum in paramagnetic oxygen and non-magnetic nitrogen lead to qualitatively different behaviour. In nitrogen, we observe the precession of the molecular angular momentum around the field vector. In oxygen, strong spin–rotation coupling results in faster and richer dynamics, encompassing the splitting of the rotation plane into three separate components. As the centrifuged molecules evolve with no significant dispersion of the molecular wave function, the observed magnetic interaction presents an efficient mechanism for controlling the plane of molecular rotation.
Zhang, Jianwei; He, Xiaodong; Yang, Lin; Wu, Guoqiang; Sha, Jianjun; Hou, Chengyu; Yin, Cunlu; Pan, Acheng; Li, Zhongzhou; Liu, Yubai
2013-01-01
The thermal conductivity of monolayer graphene nanoribbons (GNRs) with different tensile strain is investigated by using a nonequilibrium molecular dynamics method. Significant increasing amplitude of the molecular thermal vibration, molecular potential energy vibration and thermal conductivity vibration of stretching GNRs were detected. Some 20%~30% thermal conductivity decay is found in 9%~15% tensile strain of GNR cases. It is explained by the fact that GNR structural ridges scatter some low-frequency phonons which pass in the direction perpendicular to the direction of GNR stretching which was indicated by a phonon density of state investigation. PMID:23881138
Vehicle bridge interaction dynamics and potential applications
NASA Astrophysics Data System (ADS)
Yang, Y. B.; Lin, C. W.
2005-06-01
The dynamic interaction between a moving vehicle and the sustaining bridge is studied. By the method of modal superposition, closed-form solutions are obtained for the vertical responses of both the bridge and moving vehicle, assuming the vehicle/bridge mass ratio to be small. For both the bridge and vehicle responses, it is confirmed that rather accurate solutions can be obtained by considering only the first mode. The displacement, velocity, and acceleration of the bridge are governed at different extents by two sets of frequencies, i.e., the driving frequency of the vehicle and natural frequencies of the bridge. From the spectrum for the bridge displacement, the vehicle speeds can be shown to be associated with some low-frequency pikes. On the other hand, the vehicle responses are governed by five distinct frequencies that appear as driving frequencies, vehicle frequency, and bridge frequencies with shift. From the vehicle's acceleration spectrum, the first bridge frequency (with shift) is shown to have rather high visibility and can be easily identified. The effects of damping of the vehicle and bridge are evaluated in the numerical studies. Potential applications of the present results, as well as further researches required, are also indicated in the paper.
Molecular dynamics simulation of interfacial adhesion
Yarovsky, I.; Chaffee, A.L.
1996-12-31
Chromium salts are often used in the pretreatment stages of steel painting processes in order to improve adhesion at the metal oxide/primer interface. Although well established empirically, the chemical basis for the improved adhesion conferred by chromia is not well understood. A molecular level understanding of this behaviour should provide a foundation for the design of materials offering improved adhesion control. Molecular modelling of adhesion involves simulation and analysis of molecular behaviour at the interface between two interacting phases. The present study concerns behaviour at the boundary between the metal coated steel surface (with or without chromium pretreatment) and an organic primer based on a solid epoxide resin produced from bisphenol A and epichlorohydrin. An epoxy resin oligomer of molecular weight 3750 was used as the model for the primer.
Molecular Genetic Contributions to Intimate Relationship Dynamics
Saphire-Bernstein, Shimon
2015-01-01
for single polymorphisms: Toward molecular personalitysingle-handedly blazing a trail from social psychology through social neuroscience and into molecularmolecular gene was originally defined as a sequence of DNA that encodes a single
Attosecond molecular dynamics: fact or fiction?
NASA Astrophysics Data System (ADS)
Lépine, Franck; Ivanov, Misha Y.; Vrakking, Marc J. J.
2014-03-01
The emerging application of attosecond techniques to molecular systems allows the role of electronic coherence in the control of chemical reactions to be investigated. Prompt ionization of molecules by an attosecond pulse may induce charge migration across a molecular structure on attosecond to few-femtosecond timescales, thereby possibly determining the subsequent relaxation pathways that a molecule may take. We discuss how proposals for this 'charge-directed reactivity' fit within the current understanding of quantum control and review the current state of the art of attosecond molecular science. Specifically, we review the role of electronic coherence and coupling of the electronic and nuclear degrees of freedom in high-harmonic spectroscopy and in the first attosecond pump-probe experiments on molecular systems.
NASA Astrophysics Data System (ADS)
Hammes-Schiffer, Sharon; Andersen, Hans C.
1993-07-01
We present two new methods for molecular dynamics simulations based on general Hartree-Fock (GHF) theory. The first method involves approximating ab initio STO-3G matrix elements with fitting functions to enable faster computation of the energy and forces for molecular dynamics simulations. The implementation of this method includes a frozen-core approximation. The second method involves developing semiempirical potentials by reparametrizing the fitting functions obtained in the first method to fit experimental data. This second method enables us to reproduce experimental quantities with only the computational effort of an STO-3G calculation. We successfully applied both of these methods in conjunction with the Car-Parrinello ab initio molecular dynamics method to the geometry optimization of lithium clusters, cationic and neutral, of up to five atoms.
Molecular kinetic theory of boundary slip on textured surfaces by molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Wang, LiYa; Wang, FengChao; Yang, FuQian; Wu, HengAn
2014-11-01
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.
Molecular Mechanisms of Diabetic Retinopathy: Potential Therapeutic Targets
Coucha, Maha; Elshaer, Sally L.; Eldahshan, Wael S.; Mysona, Barbara A.; El-Remessy, Azza B.
2015-01-01
Diabetic retinopathy (DR) is the leading cause of blindness in working-age adults in United States. Research indicates an association between oxidative stress and the development of diabetes complications. However, clinical trials with general antioxidants have failed to prove effective in diabetic patients. Mounting evidence from experimental studies that continue to elucidate the damaging effects of oxidative stress and inflammation in both vascular and neural retina suggest its critical role in the pathogenesis of DR. This review will outline the current management of DR as well as present potential experimental therapeutic interventions, focusing on molecules that link oxidative stress to inflammation to provide potential therapeutic targets for treatment or prevention of DR. Understanding the biochemical changes and the molecular events under diabetic conditions could provide new effective therapeutic tools to combat the disease. PMID:25949069
"Roaming" dynamics in CH3CHO photodissociation revealed on a global potential energy surface.
Shepler, Benjamin C; Braams, Bastiaan J; Bowman, Joel M
2008-10-01
We present a quasiclassical trajectory study of the photodissociation of CH3CHO to molecular and radical products, CH4 + CO and CH3 + HCO, respectively, using global ab initio-based potentials energy surfaces. The molecular products have a well-defined potential barrier transition state (TS) but the dynamics exhibit strong deviations from the TS pathway to these products. The radical products are formed via a variational TS. Calculations are reported at total energies corresponding to photolysis wavelengths of 308, 282, 264, 248 and 233 nm. The results at 308 nm focus on a comparison with experiment [Houston, P. L.; Kable, S. H. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 16079] and the elucidation of the nature and extent of non-TS reaction dynamics to form the molecular products, CH4 + CO. At the other wavelengths the focus is the branching ratio of these products and the radical products, CH3 + HCO. PMID:18597443
Ab initio molecular dynamics calculations of ion hydration free energies
Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or '{lambda}-path' technique to compute the intrinsic hydration free energies of Li{sup +}, Cl{sup -}, and Ag{sup +} ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential ({phi}) contributions, we obtain absolute AIMD hydration free energies ({Delta}G{sub hyd}) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model {phi} predictions. The sums of Li{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub hyd}, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.
Molecular wire of urea in carbon nanotube: a molecular dynamics study
NASA Astrophysics Data System (ADS)
Xiu, Peng; Tu, Yusong; Tian, Xingling; Fang, Haiping; Zhou, Ruhong
2012-01-01
We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ~20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale.We perform molecular dynamics simulations of narrow single-walled carbon nanotubes (SWNTs) in aqueous urea to investigate the structure and dynamical behavior of urea molecules inside the SWNT. Even at low urea concentrations (e.g., 0.5 M), we have observed spontaneous and continuous filling of SWNT with a one-dimensional urea wire (leaving very few water molecules inside the SWNT). The urea wire is structurally ordered, both translationally and orientationally, with a contiguous hydrogen-bonded network and concerted urea's dipole orientations. Interestingly, despite the symmetric nature of the whole system, the potential energy profile of urea along the SWNT is asymmetric, arising from the ordering of asymmetric urea partial charge distribution (or dipole moment) in confined environment. Furthermore, we study the kinetics of confined urea and find that the permeation of urea molecules through the SWNT decreases significantly (by a factor of ~20) compared to that of water molecules, due to the stronger dispersion interaction of urea with SWNT than water, and a maximum in urea permeation happens around a concentration of 5 M. These findings might shed some light on the better understanding of unique properties of molecular wires (particularly the wires formed by polar organic small molecules) confined within both artificial and biological nanochannels, and are expected to have practical applications such as the electronic devices for signal transduction and multiplication at the nanoscale. Electronic supplementary information (ESI) available. See DOI: 10.1039/c1nr10793c
Lühmann, Dirk-Sören; Sengstock, Klaus
2015-01-01
In the recent years, ultracold atoms in optical lattices have proven their great value as quantum simulators for studying strongly-correlated phases and complex phenomena in solid-state systems. Here we reveal their potential as quantum simulators for molecular physics and propose a technique to image the three-dimensional molecular orbitals with high resolution. The outstanding tunability of ultracold atoms in terms of potential and interaction offer fully-adjustable model systems for gaining deep insight into the electronic structure of molecules. We study the orbitals of an artificial benzene molecule and discuss the effect of tunable interactions in its conjugated pi electron system with special regard to localization and spin order. The dynamical timescale of ultracold atom simulators are on the order milliseconds which allow for the time-resolved monitoring of a broad range of dynamical processes. As an example, we compute the hole dynamics in the conjugated pi system of the artificial benzene molecule.
Modeling ramp compression experiments using large-scale molecular dynamics simulation.
Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I.; Winey, J. Michael; Gupta, Yogendra Mohan; Lane, J. Matthew D.; Ditmire, Todd; Quevedo, Hernan J.
2011-10-01
Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.
Michael Griebel; Jan Hamaekers; Frederik Heber
2009-01-01
In this article, we examine the Young modulus of (6,m) boron–nitride nanotubes with vacancy and functionalization defects. We employ molecular dynamics simulations using the Parrinello–Rahman approach. To this end, all systems are modeled with a reactive many-body bond order Tersoff potential with parameters due to Matsunaga et al. [K. Matsunaga, Y. Iwamoto, Molecular dynamics study of atomic structure and diffusion
Dynamic Mechanism of E2020 Binding to Acetylcholinesterase: A Steered Molecular Dynamics Simulation
Sussman, Joel L.
Dynamic Mechanism of E2020 Binding to Acetylcholinesterase: A Steered Molecular Dynamics Simulation dynamics (SMD) simulations on a nanosecond scale with different velocities, and unbinding force profiles entering and leaving the TcAChE gorge. Introduction According to the cholinergic hypothesis, Alzheimer
Confirmation of anomalous dynamical arrest in attractive colloids: A molecular dynamics study
E. Zaccarelli; G. Foffi; K. A. Dawson; S. V. Buldyrev; F. Sciortino; P. Tartaglia
2002-01-01
Previous theoretical simulation and experimental studies have indicated that particles with a short-ranged attraction exhibit a range of dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singularity in the density correlation functions, and the existence of ``attractive'' and ``repulsive'' glasses. Here we carry out extensive molecular dynamics calculations on dense systems interacting via
Xin Chen; Xiliang Chen; Tao Wu; Qi Wang
2011-01-01
HIV-1 protease (HIVp) is one of the classic examples of structure-based drug design. And the dynamic structure of protein has become one of the most important characteristics that are directly related to the function of proteins. However, it is still difficult to experimentally track the specific dynamic changes in protein structure. In this work, the combination method of molecular dynamics
Xin Chen; Xiliang Chen; Tao Wu; Qi Wang
2012-01-01
HIV-1 protease (HIVp) is one of the classic examples of structure-based drug design. And the dynamic structure of protein has become one of the most important characteristics that are directly related to the function of proteins. However, it is still difficult to experimentally track the specific dynamic changes in protein structure. In this work, the combination method of molecular dynamics
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.13 Representative of this group of compounds, chlorine dioxide OClO has been the subject of much
Computation of molecular vibrational frequencies using anomalous harmoniclike potentials
NASA Astrophysics Data System (ADS)
Li, Xiangzhu; Paldus, Josef
2009-07-01
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.
What Molecular Abundances can Tell us about the Dynamics of Star Formation
NASA Astrophysics Data System (ADS)
Tassis, Konstantinos; Willacy, Karen; Yorke, Harold W.; Turner, Neal J.
2014-06-01
Molecular clouds are the sites where new stars form. Spectroscopic observations of different molecular species in these clouds can provide invaluable information regarding the dynamical evolution of star forming sites: first, they provide direct dynamical information (velocities as a function of density); second, they reveal the abundance of various molecules, which in turn depends on the chemodynamical evolutionary stage and history of the observed region. However, the connection between theoretical models of cloud dynamics and astronomical molecular spectroscopy is far from straight forward. The chemistry and dynamics of the clouds are interlinked, and various parameters such as the cloud temperature and its initial elemental abundances affect theoretical predictions, resulting in large model degeneracies: radically different dynamical models can often result in similar molecular abundances. In this talk, I will discuss first results from a massive effort undertaken to overcome this problem. By coupling non-equilibrium chemistry with a large array of different dynamical models of molecular cloud evolution, we are looking for these molecular line observables that are least affected by varying parameters and model degeneracies, and can be used to drastically constrain the possible dynamical histories of observed star-forming regions. To this end, we have studied a variety of dynamical models describing the evolution of pre- stellar molecular cloud cores (the initial phase of star formation) that cover the entire spectrum of proposed mechanisms, including pure hydrodynamical collapse and magnetically mediated collapse at various levels of importance of the magnetic field in the cloud dynamics. These models have been coupled to a network of chemical reactions that follow the relative abundances for ˜100 molecular species, by solving the non- equilibrium chemical reactions for the first time simultaneously with the dynamical equations. I will present highlights from the results of this work, including newly proposed observables with maximal potential for discrimination between different models of cloud evolution and star formation. These results are especially timely as ALMA is able to measure many of these quantities and contribute to the resolution of long-standing questions in star formation, such as the timescale of pre-stellar core evolution, and the relative importance of magnetic field and turbulence in their dynamics.
Thermal Conductivity of Natural Rubber Using Molecular Dynamics Simulation.
He, Yan; Ma, Lian-Xiang; Tang, Yuan-Zheng; Wang, Ze-Peng; Li, Wei; Kukulka, David
2015-04-01
Thermal conductivity of natural rubber has been studied by classic molecular dynamics simulations. These simulations are performed on natural rubber models using the adaptive intermolecular reactive empirical bond order (AIREBO) and the Green-Kubo molecular dynamics (MD) simulations. Thermal conductivity results are found to be very sensitive to the time step used in the simulations. For a time step of 0.1 fs, the converged thermal conductivity is 0.35 W/mK. Additionally the anisotropic thermal conductivity of a specially-modeled natural rubber model with straight molecular chains was studied and values of thermal conductivity parallel to the molecular chains was found to be 1.71 W/mK and the anisotropy, 2Kz/(Kx + Ky), was 2.67. PMID:26353571
A dielectric continuum molecular dynamics method
Massimo Marchi; Daniel Borgis; Nicolas Levy; Pietro Ballone
2001-01-01
We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of
Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars
NASA Technical Reports Server (NTRS)
Hoehler, Tori M.; Bebout, Brad M.; Visscher, Pieter T.; DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)
2000-01-01
Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.
NASA Astrophysics Data System (ADS)
Kawamoto, Shuhei; Nakamura, Takenobu; Nielsen, Steven O.; Shinoda, Wataru
2013-07-01
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
2013-07-21
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. PMID:23883011
Plasticity of metallic nanostructures : molecular dynamics simulations
Healy, Con
2014-11-27
During high speed cutting processes, metals are subject to high strains and strain rates. The dynamic nature of the deformation during high speed cutting makes it difficult to detect atomic scale deformation mechanisms ...
Ab initio QM\\/MM excited-state molecular dynamics study of coumarin 151 in water solution
Daisuke Kina; Pooja Arora; Akira Nakayama; Takeshi Noro; Mark S. Gordon; Tetsuya Taketsugu
2009-01-01
Ab initio molecular dynamics (AIMD) simulations are performed to investigate the excited state dynamics of coumarin 151 (C151) in the gas phase and in water solution at the CASSCF level of theory with segmented DZP basis sets, where in the latter case effective fragment potentials (EFP) are used. The dipole moment of an isolated C151 molecule increases considerably upon electronic
Dynamic Assessment in Educational Settings: Realising Potential.
ERIC Educational Resources Information Center
Elliott, Julian
2003-01-01
Makes the case for dynamic assessment, in which individualized instruction and feedback are built into the testing process. Urges the use of dynamic approaches to help psychologists and teachers collaborate on classroom-based interventions. Calls for studies to examine the utility of approaches. An appendix identifies target group, nature, and…
NASA Astrophysics Data System (ADS)
Kostov, Konstantin S.; Freed, Karl F.; Webb, Edmund B.; Mondello, Maurizio; Grest, Gary S.
1998-06-01
Molecular dynamics (MD) simulations of united atom models for alkane melts are compared with a recently developed theory for calculating the memory functions of flexible polymers. The theory is based upon an approximate solution of the diffusion equation without hydrodynamic interactions. The polymer dynamics are described by using time correlation functions which are expressed in terms of a set of equilibrium averages and the approximate eigenvalues and eigenfunctions of the diffusion operator. For flexible enough chains with sufficiently high molecular weight, the hydrodynamic interactions are screened, and the simplified solvent model used by the theory is expected to be adequate. The only parameter not defined by the MD simulations is the bead friction coefficient ?. In the limit of weak hydrodynamic interactions (Rouse dynamics), ? can be determined from the molecular diffusion coefficient by applying the Rouse relation D=kT/N?R. Given this choice of ?R, the time correlation functions computed from the theory are compared with those obtained directly from the MD simulations. Excellent agreement with the simulations is found for all correlation functions and all times for the decane dynamics, provided the theory employs one scale factor to increase ?R and, hence, to compensate for the inadequacy of the Rouse relation. The same picture holds for hexadecane and triacontane (C30H62) but with smaller scale factors. Scaling becomes unnecessary for C44H90 which is long enough for the crossover to Rouse dynamics for D to be almost complete. Very good agreement (after appropriate scaling of ?R) also emerges between theory and simulations for several branched alkanes with carbon numbers C25-C30. Computations for hexadecane at different temperatures show that the scale factors may be weakly temperature dependent.
Structure and Dynamics of Magnetized Dark Molecular Clouds
NASA Astrophysics Data System (ADS)
Li, P. S.; McKee, C. F.; Klein, R. I.
2015-03-01
Massive infrared dark clouds (IRDCs) are believed to be the precursors to star clusters and massive stars (e.g. Bergin & Tafalla 2007). The supersonic, turbulent nature of molecular clouds in the presence of magnetic fields poses a great challenge in understanding the structure and dynamics of magnetized molecular clouds and the star formation therein. Using the high-order radiation-magneto-hydrodynamic adaptive mesh refinement (AMR) code ORION2 (Li et al. 2012), we perform a large-scale driven-turbulence simulation to reveal the 3D filamentary structure and dynamical state of a highly supersonic (thermal Mach number = 10) and strongly magnetized (plasma ?=0.02) massive infrared dark molecular cloud. With the high resolution afforded by AMR, we follow the dynamical evolution of the cloud in order to understand the roles of strong magnetic fields, turbulence, and self-gravity in shaping the cloud and in the formation of dense cores.
Spatio-temporal dynamics of optical molecular motors
NASA Astrophysics Data System (ADS)
Gehrig, Edeltraud; Hess, Ortwin
2004-09-01
Molecular motors are multicomponent molecular structures that consume energy to induce motion and to generate forces. Their dynamics covers various time and length scales and critically depends on chemical-mechanical coupling, external forces and molecular properties such as diffusion, particle distribution and density. The complex behavior of these systems consequently offers a formidable challenge for theoretical descriptions and numerical approaches that aim to provide a computational laboratory for a fundamental analysis of the underlying interaction mechanisms as well as interpretations or to study control of the system's behavior. Coupling a linear molecular motor system to an energy supply can induce movement of the motor molecules along a filamentous structure. The complex dynamics of bound (i.e. attached to a filament) and free (i.e. diffusing in the surrounding medium) molecular motors thereby may depend on the diffusive properties of the molecules and on the excitation process driving the motor system. Our theory is therefore based on spatially dependent Fokker-Planck equations for the dynamics of bound and free motors. The model considers spatially inhomogeneous transition rates coupling the energetic sublebels of the molecules as well as spatial fluctuations and diffusion. Computational modelling of the spatio-temporal dynamics of molecular motors shows that both, molecular diffusion and bandwidth of the transition rate set an upper limit to the efficiency of the motor progression. A sufficiently small molecular diffusion as well as a thorough adjustment of transition rates lead to a regular forward propagation while for high diffusion and improperly chosen rates spatio-temporally diverging particle distributions may evolve. Suitable excitation conditions for efficient movement-control are discussed.
Sugar Transport across Lactose Permease Probed by Steered Molecular Dynamics
Morten Ø. Jensen; Ying Yin; Emad Tajkhorshid; Klaus Schulten
2007-01-01
Escherichia coli lactose permease (LacY) transports sugar across the inner membrane of the bacterium using the proton motive force to accumulate sugar in the cytosol. We have probed lactose conduction across LacY using steered molecular dynamics, permitting us to follow molecular and energetic details of lactose interaction with the lumen of LacY during its permeation. Lactose induces a widening of
RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.
Leonarski, Filip; Trylska, Joanna
2015-04-21
Coarse-grained (CG) models in molecular dynamics (MD) are powerful tools to simulate the dynamics of large biomolecular systems on micro- to millisecond timescales. However, the CG model, potential energy terms, and parameters are typically not transferable between different molecules and problems. So parameterizing CG force fields, which is both tedious and time-consuming, is often necessary. We present RedMDStream, a software for developing, testing, and simulating biomolecules with CG MD models. Development includes an automatic procedure for the optimization of potential energy parameters based on metaheuristic methods. As an example we describe the parameterization of a simple CG MD model of an RNA hairpin. PMID:25902423
Molecular dynamics simulation studies of liquid crystalline materials
NASA Astrophysics Data System (ADS)
Tian, Pu
Molecular dynamics (MD) simulation studies of the phase behavior, the response to an applied field of nematic liquid crystalline (LC) materials and interactions of nanoparticles in isotropic mesogenic materials are presented in this work. Molecular models used include the rigid bead-necklace model and soft spherocylinders. Free energy calculations applying thermodynamic integration and the Gibbs-Duhem integration method were used to establish the (T, P) phase diagram of the repulsive bead-necklace model, subsequently the Gibbs-Duhem integration method was further utilized to investigate the influence of attractive interactions on the phase behavior of the bead-necklace model. Analysis of order and thermodynamics of LC phase transitions (Isotropic-Nematic transition and Nematic-Smectic A transition) demonstrate that this simple model can capture the basic physics of liquid crystalline phases, and good agreement with experimental results is obtained. Further addition of chemical details to this multiple interaction sites model is much easier than to the idealized models (Gay-Berne, Spherocylinders) while the computation cost increase with respect to these idealized models is minimal. With a mean field representation of field-molecules interaction, MD simulation studies of the switching behavior of nematic LC, which is the basis of many LC devices, were performed. The switching mechanisms were explained in terms of the compromise between the elastic energy and field-molecules interactions. Qualitative agreement with experiments confirmed the validity of the mean field approximation. Finally, using the standard umbrella sampling technique and MD simulations, the potential of mean force between two nanoparticles in solvent of spherocylinders is calculated. It is found that while dispersed nanoparticles will delay the Isotropic-Nematics transition to higher density (lower temperature), they can induce local ordering fluctuations (within a few molecular lengths of the solvent rods), which are different from natural paranematic fluctuations by faster decay with respect to distance and broader distribution of local ordering. Apart from the expected short ranged nanoparticle interactions due to molecular packing effects, the above mentioned induced fluctuations will cause long range repulsions, a novel interaction being discovered and characterized for the first time.
White, Stephen
of the molecular components underly- ing the profile (6). Molecular dynamics simulations used in concertDiffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics, Gaithersburg, Maryland ABSTRACT We have recently shown that current molecular dynamics (MD) atomic force fields
Chinnasamy, Sathishkumar; Chinnasamy, Selvakkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan
2015-01-01
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
NASA Astrophysics Data System (ADS)
Ryltsev, R. E.; Chtchelkatchev, N. M.; Ryzhov, V. N.
2013-01-01
We investigate glassy dynamical properties of one-component three-dimensional system of particles interacting via pair repulsive potential by the molecular dynamic simulation in the wide region of densities. The glass state is superfragile and it has high glass-forming ability. The glass transition temperature Tg has a pronounced minimum at densities where the frustration is maximal.
Ryltsev, R E; Chtchelkatchev, N M; Ryzhov, V N
2013-01-11
We investigate glassy dynamical properties of one-component three-dimensional system of particles interacting via pair repulsive potential by the molecular dynamic simulation in the wide region of densities. The glass state is superfragile and it has high glass-forming ability. The glass transition temperature T(g) has a pronounced minimum at densities where the frustration is maximal. PMID:23383914
AceCloud: Molecular Dynamics Simulations in the Cloud.
Harvey, M J; De Fabritiis, G
2015-05-26
We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services. PMID:25849093
Dynamic Nanodevices Based on Protein Molecular Motors
Dan V. Nicolau
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
NASA Astrophysics Data System (ADS)
Karthick, T.; Balachandran, V.; Perumal, S.
2015-04-01
Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm-1 has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation.
Karthick, T; Balachandran, V; Perumal, S
2015-04-15
Thiophene derivatives have been focused in the past decades due to their remarkable biological and pharmacological activities. In connection with that the conformational stability, spectroscopic characterization, molecular (inter- and intra-) interactions, and molecular docking studies on thiophene-2-carboxylicacid have been performed in this work by experimental FT-IR and theoretical quantum chemical computations. Experimentally recorded FT-IR spectrum in the region 4000-400 cm(-1) has been compared with the scaled theoretical spectrum and the spectral peaks have been assigned on the basis of potential energy distribution results obtained from MOLVIB program package. The conformational stability of monomer and dimer conformers has been examined. The presence of inter- and intramolecular interactions in the monomer and dimer conformers have been explained by natural bond orbital analysis. The UV-Vis spectra of the sample in different solvents have been simulated and solvent effects were predicted by polarisable continuum model with TD-DFT/B3LYP/6-31+G(d,p) method. To test the biological activity of the sample, molecular docking (ligand-protein) simulations have been performed using SWISSDOCK web server. The full fitness (FF) score and binding affinity values revealed that thiophene-2-carboxylicacid can act as potential inhibitor against inflammation. PMID:25677530
Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine
2012-05-25
GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach. PMID:22462609
Han, Sanghwa
2008-12-12
Estimation of structural perturbation induced by S-nitrosation is important to understand the mode of cellular signal transduction mediated by nitric oxide. Crystal structures of S-nitrosated proteins have been solved only for a few cases, however, so that molecular dynamics simulation may provide an alternative tool for probing structural perturbation. In this study AMBER-99 force field parameters for S-nitrosocysteine were developed and applied to molecular dynamics simulations of S-nitrosated thioredoxin. Geometry optimization at the level of HF/6-31G* was followed by a restrained electrostatic potential charge-fitting to obtain the atomic charges of S-nitrosocysteine. Force constants for bonds and angles were obtained from generalized AMBER force field. Torsional force constants for CC-SN and CS-NO were determined by fitting the torsional profiles obtained from geometry optimization with those from molecular mechanical energy minimization. Finally molecular dynamics simulations were performed with theses parameters on oxidized and reduced thioredoxin with and without S-nitrosocysteine. In all cases the root-mean-square deviations of {alpha}-carbons yielded well-behaved trajectories. The CC-SH dihedral angle which fluctuated severely during the simulation became quiet upon S-nitrosation. In conclusion the force field parameters developed in this study for S-nitrosocysteine appear to be suitable for molecular dynamics simulations of S-nitrosated proteins.
Dynamical effects in electron tunnelling: Nonlocal image potentials
NASA Astrophysics Data System (ADS)
Tran Thoai, D. B.; Šunji?, M.
1991-03-01
We generalize Jonson's nonlocal theory of dynamical exchange-correlation potential in tunnelling to the metal-insulator-metal (M-I-M) case, for zero and nonzero tunnelling currents, and solve in the second order exactly including surface effects. The correct treatment removes unphysical features near interfaces. The nonlocal calculation gives dynamical image potentials reduced in comparison to the classical image potential, but this reduction is less drastic than in the local approximation.
Molecular Dynamics Simulation of Sintering Dynamics of Many TiO Nanoparticles
NASA Astrophysics Data System (ADS)
Mao, Qian; Luo, K. H.
2015-09-01
The sintering processes of many TiO nanoparticles in chains of both solid and liquid phases have been studied in detail via molecular dynamics simulation. For the liquid phase, a modified correlation for the characteristic sintering time of multi-particle chains is obtained by including a correction factor of , where N is the number of primary particles. The temperature rise during sintering is found to be linearly proportional to . Moreover, this study provides a way to calculate the surface energy of nanoparticles of small diameters in liquid phase, which is experimentally unattainable. For the solid phase, sintering induced nucleation is observed for cases both at and 960 K with a sharp increase in the temperature and a decrease in the potential energy. The formation of rutile from nucleation of many solid amorphous particles through sintering is observed for the first time.
MOLECULAR DYNAMICS: Biomolecules See the Light
NSDL National Science Digital Library
David W. Pratt (University of Pittsburgh; Department of Chemistry)
2002-06-28
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.
Nonadiabatic Molecular Dynamics Simulation of Light-Induced Electron Transfer from an Anchored Molecular Electron Donor to a Semiconductor Acceptor William Stier and Oleg V. Prezhdo* Department Form: February 21, 2002 A nonadiabatic molecular dynamics (MD) simulation of the photoinduced electron
Molecular dynamics modelling of radiation damage in zircon
NASA Astrophysics Data System (ADS)
Grechanovsky, A. E.
2009-04-01
Zircon (ZrSiO4) is among actinide-bearing phases which has been proposed as a crystalline confinement matrix for nuclear waste management, especially for weapon-grade plutonium and UO2 spent fuel in the USA. Zircon is also widely used in geochronology. But, with accumulating ?-decay damage, zircon undergoes a radiation induced transition to an amorphous (or metamict) state. So, in the present work molecular dynamics simulations (MD simulations) of zircon structure have been performed to study radiation damage in zircon. In this technique, one simulates the propagation of an energetic particle in a system of atoms interacting via model potentials, by integrating the Newton equations of motion. Author has used version 3.09 of the DL_POLY molecular simulation package. Zircon structure containing 181944 atoms (19x19x21 unit cells) was equilibrated at 300 K for 10 ps, and one Zr atom (usually called the primary knock-on atom, PKA) was given a velocity corresponding to an implantation energy of about 20 keV. MD simulations were performed in the microcanonical ensemble that is under conditions of constant particle number, volume and energy. Results of the MD simulations show that the number of interstitials is equal to 840 atoms. This is very close (4000-5000 atoms for 70 keV recoil atom 234Th) to what is measured in the diffuse x-ray scattering and NMR experiments on amorphous metamict samples (damaged by natural irradiation) of geological age. It has been shown that the damaged structure contains several depleted regions with characteristic sized up to 2,5 nm after single event and up to 4,5 nm after three overlapping events. Furthermore, these events produce channels of depleted matter between the overlapping damaged regions. These channels provide a high-diffusivity path for radiogenic Pb (percolation effect). Loss of radiogenic Pb may result in to incorrect dating of rocks.
MDVRY: a polarizable classical molecular dynamics package for biomolecules
M. Souaille; H. Loirat; D. Borgis; M. P. Gaigeot
2009-01-01
The MDVRY classical molecular dynamics package is presented for the study of biomolecules in the gas and liquid phase. Electrostatic polarization has been implemented in the formalism of point induced dipoles following the model of Thole. Two schemes have been implemented for the calculation of induced dipoles, i.e. resolution of the self-consistent equations and a ‘Car–Parrinello’ dynamical approach. In this
Imaging the molecular dynamics of dissociative electron attachment to water
Adaniya, Hidihito; Rudek, B.; Osipov, Timur; Haxton, Dan; Weber, Thorsten; Rescigno, Thomas N.; McCurdy, C.W.; Belkacem, Ali
2009-10-19
Momentum imaging experiments on dissociative electron attachment to the water molecule are combined with ab initio theoretical calculations of the angular dependence of the quantum mechanical amplitude for electron attachment to provide a detailed picture of the molecular dynamics of dissociation attachment via the two lowest energy Feshbach resonances. The combination of momentum imaging experiments and theory can reveal dissociation dynamics for which the axial recoil approximation breaks down and thus provides a powerful reaction microscope for DEA to polyatomics.
A fast recursive algorithm for molecular dynamics simulation
NASA Technical Reports Server (NTRS)
Jain, A.; Vaidehi, N.; Rodriguez, G.
1993-01-01
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.
Plastic dislocation motion via nonequilibrium molecular and continuum dynamics
Hoover, W.G.; Ladd, A.J.C.; Hoover, N.E.
1980-09-29
The classical two-dimensional close-packed triangular lattice, with nearest-neighbor spring forces, is a convenient standard material for the investigation of dislocation motion and plastic flow. Two kinds of calculations, based on this standard material, are described here: (1) Molecular Dynamics simulations, incorporating adiabatic strains described with the help of Doll's Tensor, and (2) Continuum Dynamics simulations, incorporating periodic boundaries and dislocation interaction through stress-field superposition.
Analytical formulation for soliton-potential dynamics
Kurosh Javidan
2009-01-15
An analytical model for the soliton-potential interaction is presented, by constructing a collective coordinate for the system. Most of the characters of the interaction are derived analytically while they are calculated by other models numerically. We will find that the behaviour of the soliton is like a point particle living under the influence of a complicated potential which is a function of soliton velocity and the potential parameters. The analytic model does not have a clear prediction for the islands of initial velocities in which the soliton may reflect back or escape over the potential well.
Molecular Dynamics Simulation of Amyloid ? Dimer Formation
B. Urbanc; L. Cruz; F. Ding; D. Sammond; S. Khare; S. V. Buldyrev; H. E. Stanley; N. V. Dokholyany
2004-01-01
Recent experiments with amyloid ? (A?) peptide indicate that formation of toxic oligomers may be an important contribution to the onset of Alzheimer's disease. The toxicity of A? oligomers depends on their structure, which is governed by assembly dynamics. Due to limitations of current experimental techniques, a detailed knowledge of oligomer structure at the atomic level is missing. We introduce
Molecular dynamics simulation of intrinsically disordered proteins
Anna Battisti; Alexander Tenenbaum
2012-01-01
Intrinsically disordered proteins are biomolecules that do not have a definite 3D structure; therefore, their dynamical simulation cannot start from a known list of atomistic positions, such as a Protein Data Bank file. We describe a method to start a computer simulation of these proteins. The first step of the procedure is the creation of a multi-rod configuration of the
Molecular dynamics simulation of intrinsically disordered proteins
Anna Battisti; Alexander Tenenbaum
2011-01-01
Intrinsically disordered proteins are biomolecules that do not have a definite 3D structure; therefore, their dynamical simulation cannot start from a known list of atomistic positions, such as a Protein Data Bank file. We describe a method to start a computer simulation of these proteins. The first step of the procedure is the creation of a multi-rod configuration of the
Molecular Mechanotransduction: how forces trigger cytoskeletal dynamics
NASA Astrophysics Data System (ADS)
Ehrlicher, Allen
2012-02-01
Mechanical stresses elicit cellular reactions mediated by chemical signals. Defective responses to forces underlie human medical disorders, such as cardiac failure and pulmonary injury. Despite detailed knowledge of the cytoskeleton's structure, the specific molecular switches that convert mechanical stimuli into chemical signals have remained elusive. Here we identify the actin-binding protein, filamin A (FLNa) as a central mechanotransduction element of the cytoskeleton by using Fluorescence Loss After photoConversion (FLAC), a novel high-speed alternative to FRAP. We reconstituted a minimal system consisting of actin filaments, FLNa and two FLNa-binding partners: the cytoplasmic tail of ß-integrin, and FilGAP. Integrins form an essential mechanical linkage between extracellular and intracellular environments, with ß integrin tails connecting to the actin cytoskeleton by binding directly to filamin. FilGAP is a FLNa-binding GTPase-activating protein specific for Rac, which in vivo regulates cell spreading and bleb formation. We demonstrate that both externally-imposed bulk shear and myosin II driven forces differentially regulate the binding of integrin and FilGAP to FLNa. Consistent with structural predictions, strain increases ß-integrin binding to FLNa, whereas it causes FilGAP to dissociate from FLNa, providing a direct and specific molecular basis for cellular mechanotransduction. These results identify the first molecular mechanotransduction element within the actin cytoskeleton, revealing that mechanical strain of key proteins regulates the binding of signaling molecules. Moreover, GAP activity has been shown to switch cell movement from mesenchymal to amoeboid motility, suggesting that mechanical forces directly impact the invasiveness of cancer.
Dynamical Higgs potentials with a landscape
J. L. F. Barbon; C. Hoyos
2006-02-28
We consider one-loop effective potentials for adjoint Higgs fields that originate from flat holonomies in toroidal compactification of gauge theories. We show that such potentials are "landscape-like" for large gauge groups and generic non-supersymmetric matter representations. In particular, there is a large number of vacua with similar local properties, scanning a broad band of vacuum energies.