Molecular dynamics computer simulation of scratch resistance testing of polymers: visualization

Experimental scratch resistance testing provides two numbers: the penetration depth Rp and the healing depth Rh. In molecular dynamics computer simulations, we create a material consisting of N statistical chain segments by polymerization; a reinforcing phase can be included. Then we simulate the movement of an indenter and response of the segments during X time steps. Each segment at each time step has three Cartesian coordinates of position and three of momentum. We describe methods of visualization of results based on a record of 6NX coordinates. We obtain a continuous dependence on time t of positions of each of the segments on the path of the indenter. Scratch resistance at a given location can be connected to spatial structures of individual polymeric chains.

Diffusive transport properties in monovalent and divalent metal-ion halide melts: A computer simulation study

Self- and cross-velocity correlation functions and related transport coefficients of molten salts are studied by molecular-dynamics simulation. Six representative systems are considered, i.e., NaCl and KCl alkali halides, CuCl and CuBr noble-metal halides, and SrCl2 and ZnCl2 divalent metal-ion halides. Computer simulation results are compared with experimental self-diffusion coefficients and electrical conductivities. Special attention is paid to dynamic cross correlations and their dependence on the Coulomb interactions as well as on the size and mass differences between anions and cations.

Diffusive transport properties in monovalent and divalent metal-ion halide melts: A computer simulation study

Self- and cross-velocity correlation functions and related transport coefficients of molten salts are studied by molecular-dynamics simulation. Six representative systems are considered, i.e., NaCl and KCl alkali halides, CuCl and CuBr noble-metal halides, and SrCl2 and ZnCl2 divalent metal-ion halides. Computer simulation results are compared with experimental self-diffusion coefficients and electrical conductivities. Special attention is paid to dynamic cross correlations and their dependence on the Coulomb interactions as well as on the size and mass differences between anions and cations.

Computer simulation of the effect of cargo shifting on articulated vehicles performing braking and cornering maneuvers. Volume 1: executive summary. Final report.

Federal Highway Administration, Structures and Applied Mechanics Division, Washington, D.C.

Computer simulation of the effect of cargo shifting on articulated vehicles performing braking and cornering maneuvers. Volume 2: technical report. Final report.

Federal Highway Administration, Structures and Applied Mechanics Division, Washington, D.C.

Computer simulation of the effect of cargo shifting on articulated vehicles performing braking and cornering maneuvers. Volume 4: user's manual for TDVS/SLOSH. Final report.

Federal Highway Administration, Structures and Applied Mechanics Division, Washington, D.C.

Computer simulation of the effect of cargo shifting on articulated vehicles performing braking and cornering maneuvers. Volume 3: technical supplement. Final report.

Federal Highway Administration, Structures and Applied Mechanics Division, Washington, D.C.

Computer simulation study of collective dynamics in the glass former Ca(NO3)(2)center dot 4H(2)O

Time correlation functions of current fluctuations were calculated by molecular dynamics (MD) simulations in order to investigate sound waves of high wavevectors in the glass-forming liquid Ca(NO3)(2)center dot 4H(2)O. Dispersion curves, omega(k), were obtained for longitudinal (LA) and transverse acoustic (TA) modes, and also for longitudinal optic (LO) modes. Spectra of LA modes calculated by MD simulations were modeled by a viscoelastic model within the memory function framework. The viscoelastic model is used to rationalize the change of slope taking place at k similar to 0.3 angstrom(-1) in the omega(k) curve of acoustic modes. For still larger wavevectors, mixing of acoustic and optic modes is observed. Partial time correlation functions of longitudinal mass currents were calculated separately for the ions and the water molecules. The wavevector dependence of excitation energies of the corresponding partial LA modes indicates the coexistence of a relatively stiff subsystem made of cations and anions, and a softer subsystem made of water molecules. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4751548]

Computer simulation of ordering and dynamics in liquid crystals in the bulk and close to the surface

The aim of this PhD thesis is to investigate the orientational and dynamical properties of liquid crystalline systems, at molecular level and using atomistic computer simulations, to reach a better understanding of material behavior from a microscopic point view. In perspective this should allow to clarify the relation between the micro and macroscopic properties with the objective of predicting or confirming experimental results on these systems. In this context, we developed four different lines of work in the thesis. The first one concerns the orientational order and alignment mechanism of rigid solutes of small dimensions dissolved in a nematic phase formed by the 4-pentyl,4 cyanobiphenyl (5CB) nematic liquid crystal. The orientational distribution of solutes have been obtained with Molecular Dynamics Simulation (MD) and have been compared with experimental data reported in literature. we have also verified the agreement between order parameters and dipolar coupling values measured in NMR experiments. The MD determined effective orientational potentials have been compared with the predictions of Maier­Saupe and Surface tensor models. The second line concerns the development of a correct parametrization able to reproduce the phase transition properties of a prototype of the oligothiophene semiconductor family: sexithiophene (T6). T6 forms two crystalline polymorphs largely studied, and possesses liquid crystalline phases still not well characterized, From simulations we detected a phase transition from crystal to liquid crystal at about 580 K, in agreement with available experiments, and in particular we found two LC phases, smectic and nematic. The crystal­smectic transition is associated to a relevant density variation and to strong conformational changes of T6, namely the molecules in the liquid crystal phase easily assume a bent shape, deviating from the planar structure typical of the crystal. The third line explores a new approach for calculating the viscosity in a nematic through a virtual exper- iment resembling the classical falling sphere experiment. The falling sphere is replaced by an hydrogenated silicon nanoparticle of spherical shape suspended in 5CB, and gravity effects are replaced by a constant force applied to the nanoparticle in a selected direction. Once the nanoparticle reaches a constant velocity, the viscosity of the medium can be evaluated using Stokes' law. With this method we successfully reproduced experimental viscosities and viscosity anisotropy for the solvent 5CB. The last line deals with the study of order induction on nematic molecules by an hydrogenated silicon surface. Gaining predicting power for the anchoring behavior of liquid crystals at surfaces will be a very desirable capability, as many properties related to devices depend on molecular organization close to surfaces. Here we studied, by means of atomistic MD simulations, the flat interface between an hydrogenated (001) silicon surface in contact with a sample of 5CB molecules. We found a planar anchoring of the first layers of 5CB where surface interactions are dominating with respect to the mesogen intermolecular interactions. We also analyzed the interface 5CB­vacuum, finding a homeotropic orientation of the nematic at this interface.

A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins

Signal proteins are able to adapt their response to a change in the environment, governing in this way a broad variety of important cellular processes in living systems. While conventional molecular-dynamics (MD) techniques can be used to explore the early signaling pathway of these protein systems at atomistic resolution, the high computational costs limit their usefulness for the elucidation of the multiscale transduction dynamics of most signaling processes, occurring on experimental timescales. To cope with the problem, we present in this paper a novel multiscale-modeling method, based on a combination of the kinetic Monte-Carlo- and MD-technique, and demonstrate its suitability for investigating the signaling behavior of the photoswitch light-oxygen-voltage-2-Jα domain from Avena Sativa (AsLOV2-Jα) and an AsLOV2-Jα-regulated photoactivable Rac1-GTPase (PA-Rac1), recently employed to control the motility of cancer cells through light stimulus. More specifically, we show that their signaling pathways begin with a residual re-arrangement and subsequent H-bond formation of amino acids near to the flavin-mononucleotide chromophore, causing a coupling between β-strands and subsequent detachment of a peripheral α-helix from the AsLOV2-domain. In the case of the PA-Rac1 system we find that this latter process induces the release of the AsLOV2-inhibitor from the switchII-activation site of the GTPase, enabling signal activation through effector-protein binding. These applications demonstrate that our approach reliably reproduces the signaling pathways of complex signal proteins, ranging from nanoseconds up to seconds at affordable computational costs.

High-resolution computer simulation of the dynamics of isoelectric focusing using carrier ampholytes: focusing with concurrent electrophoretic mobilization is an isotachophoretic process

Focusing of four hemoglobins with concurrent electrophoretic mobilization was studied by computer simulation. A dynamic electrophoresis simulator was first used to provide a detailed description of focusing in a 100-carrier component, pH 6-8 gradient using phosphoric acid as anolyte and NaOH as catholyte. These results are compared to an identical simulation except that the catholyte contained both NaOH and NaCl. A stationary, steady-state distribution of carrier components and hemoglobins is produced in the first configuration. In the second, the chloride ion migrates into and through the separation space. It is shown that even under these conditions of chloride ion flux a pH gradient forms. All amphoteric species acquire a slight positive charge upon focusing and the whole pattern is mobilized towards the cathode. The cathodic gradient end is stable whereas the anodic end is gradually degrading due to the continuous accumulation of chloride. The data illustrate that the mobilization is a cationic isotachophoretic process with the sodium ion being the leading cation. The peak height of the hemoglobin zones decreases somewhat upon mobilization, but the zones retain a relatively sharp profile, thus facilitating detection. The electropherograms that would be produced by whole column imaging and by a single detector placed at different locations along the focusing column are presented and show that focusing can be commenced with NaCl present in the catholyte at the beginning of the experiment. However, this may require detector placement on the cathodic side of the catholyte/sample mixture interface.

High-resolution computer simulation of the dynamics of isoelectric focusing: in quest of more realistic input parameters for carrier ampholytes

The impact of the systematic variation of either DeltapK(a) or mobility of 140 biprotic carrier ampholytes on the conductivity profile of a pH 3-10 gradient was studied by dynamic computer simulation. A configuration with the greatest DeltapK(a) in the pH 6-7 range and uniform mobilities produced a conductivity profile consistent with that which is experimentally observed. A similar result was observed when the neutral (pI = 7) ampholyte is assigned the lowest mobility and mobilities of the other carriers are systematically increased as their pI's recede from 7. When equal DeltapK(a) values and mobilities are assigned to all ampholytes a conductivity plateau in the pH 5-9 region is produced which does not reflect what is seen experimentally. The variation in DeltapK(a) values is considered to most accurately reflect the electrochemical parameters of commercially available mixtures of carrier ampholytes. Simulations with unequal mobilities of the cationic and anionic species of the carrier ampholytes show either cathodic (greater mobility of the cationic species) or anodic (greater mobility of the anionic species) drifts of the pH gradient. The simulated cationic drifts compare well to those observed experimentally in a capillary in which the focusing of three dyes was followed by whole column optical imaging. The cathodic drift flattens the acidic portion of the gradient and steepens the basic part. This phenomenon is an additional argument against the notion that focused zones of carrier ampholytes have no electrophoretic flux.

Computer Simulation of Crowd Dynamics and Destructive Crowd Behavior

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the area of a riot engages in violence, and those who do, do not do so continuously. Instead, small groups carry out the majority of violent acts in relatively short-lived episodes. Agent-based computer simulations are an ideal method for modeling complex group-level social phenomena, such as celebratory gatherings and riots, which emerge from the interaction of relatively “simple” individuals. By making simple assumptions about individuals’ decision-making and behaviors and allowing actors to affect one another, behavioral patterns emerge that cannot be predicted by the characteristics of individuals. The computer simulation developed here models celebratory riot behavior by repeatedly evaluating a single algorithm for each individual, the inputs of which are affected by the characteristics of nearby actors. Specifically, the simulation assumes that (a) actors possess 1 of 5 distinct social identities (group memberships), (b) actors will congregate with actors who possess the same identity, (c) the degree of social cohesion generated in the social context determines the stability of relationships within groups, and (d) actors’ level of aggression is affected by the aggression of other group members. Not only does this simulation provide a systematic investigation of the effects of the initial distribution of aggression, social identification, and cohesiveness on riot outcomes, but also an analytic tool others may use to investigate, visualize and predict how various individual characteristics affect emergent crowd behavior.

Computer simulation of the effect of road roughness on tire-pavement forces in braking and cornering. Interim report.

Federal Highway Administration, Washington, D.C.