Coarse-Grained Chemical Reaction Model

Biomimetic Coatings Obtained by Combinatorial Laser Technologies

The modification of implant devices with biocompatible coatings has become necessary as a consequence of premature loosening of prosthesis. This is caused mainly by chronic inflammation or allergies that are triggered by implant wear, production of abrasion particles, and/or release of metallic ions from the implantable device surface. Specific to the implant tissue destination, it could require coatings with specific features in order to provide optimal osseointegration. Pulsed laser deposition (PLD) became a well-known physical vapor deposition technology that has been successfully applied to a large variety of biocompatible inorganic coatings for biomedical prosthetic applications. Matrix assisted pulsed laser evaporation (MAPLE) is a PLD-derived technology used for depositions of thin organic material coatings. In an attempt to surpass solvent related difficulties, when different solvents are used for blending various organic materials, combinatorial MAPLE was proposed to grow thin hybrid coatings, assembled in a gradient of composition. We review herein the evolution of the laser technological process and capabilities of growing thin bio-coatings with emphasis on blended or multilayered biomimetic combinations. These can be used either as implant surfaces with enhanced bioactivity for accelerating orthopedic integration and tissue regeneration or combinatorial bio-platforms for cancer research.

A molecular dynamics study of the effects of the inclusion of dopants on ablation in polymethyl methacrylate

Molecular dynamics simulations are used to elucidate mechanisms of ablation in dopant-polymer systems. In one set of simulations, a uniform distribution of thermal absorbers are added to a polymethyl methacrylate substrate and are excited. Chemical decomposition occurs in the regions near the absorbers. Ejection of large pieces of substrate then follows the thermo-chemical breakdown of material. In another set of simulations, an absorbing cluster is embedded in the polymethyl methacrylate substrate at a depth of 50 or 250 A. Only the particles comprising the cluster are excited during the laser pulse. Ejection of material is initiated upon the fracture of the cluster and the cleavage of the surrounding polymer bonds with little chemical damage during the process. These two mechanisms of ejection suggest different pathways of ablation in doped polymer materials.

Elucidating the thermal, chemical, and mechanical mechanisms of ultraviolet ablation in poly(methyl methacrylate) via molecular dynamics simulations

[Figure: see text]. Laser ablation harnesses photon energy to remove material from a surface. Although applications such as laser-assisted in situ keratomileusis (LASIK) surgery, lithography, and nanoscale device fabrication take advantage of this process, a better understanding the underlying mechanism of ablation in polymeric materials remains much sought after. Molecular simulation is a particularly attractive technique to study the basic aspects of ablation because it allows control over specific process parameters and enables observation of microscopic mechanistic details. This Account describes a hybrid molecular dynamics-Monte Carlo technique to simulate laser ablation in poly(methyl methacrylate) (PMMA). It also discusses the impact of thermal and chemical excitation on the ensuing ejection processes. We used molecular dynamics simulation to study the molecular interactions in a coarse-grained PMMA substrate following photon absorption. To ascertain the role of chemistry in initiating ablation, we embedded a Monte Carlo protocol within the simulation framework. These calculations permit chemical reactions to occur probabilistically during the molecular dynamics calculation using predetermined reaction pathways and Arrhenius rates. With this hybrid scheme, we can examine thermal and chemical pathways of decomposition separately. In the simulations, we observed distinct mechanisms of ablation for each type of photoexcitation pathway. Ablation via thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case in which an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. A detailed analysis of the processes shows that a critical energy for ablation can describe this complex series of events. The simulations show a decrease in the critical energy with a greater amount of photochemistry. Additionally, the simulations demonstrate the effects of the energy deposition rate on the ejection mechanism. When the energy is deposited rapidly, not allowing for mechanical relaxation of the sample, the formation of a pressure wave and subsequent tensile wave dominates the ejection process. This study provides insight into the influence of thermal, chemical, and mechanical processes in PMMA and facilitates greater understanding of the complex nature of polymer ablation. These simulations complement experiments that have used chemical design to harness the photochemical properties of materials to enhance laser ablation. We successfully fit the results of the simulations to established analytical models of both photothermal and photochemical ablation and demonstrate their relevance. Although the simulations are for PMMA, the mechanistic concepts are applicable to a large range of systems and provide a conceptual foundation for interpretation of experimental data.

Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials

The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.

Effect of cluster size in kiloelectronvolt cluster bombardment of solid benzene

Emission of benzene molecules by 5-keV cluster bombardment of a range of carbon projectiles from C6H6 to C180 is studied by a coarse-grained molecular dynamics (MD) technique. This approach permits calculations that are not feasible using more complicated potential energy functions, particularly as the interesting physics associated with the ion impact event approaches the mesoscale. These calculations show that the highest ejection yields are associated with clusters that deposit their incident energy 15-20 A below the surface. The highest yield for the projectiles is produced by the C20 and C60 projectiles. The results from the MD simulations are also compared favorably to an analytical model based on fluid dynamics to describe the energy deposition. The analytical model is then utilized to extend the range of the calculations to higher incident energies. The issue of the relative amount of chemical fragmentation and intact molecular desorption is also examined for the benzene crystal. These results show that damage accumulation at high-incident fluence should not be problematic and that it should be possible to perform molecular depth profiling via secondary ion mass spectrometry experiments. In general, the approach presented here illustrates the power of combining a simplified MD method with analytical strategies for describing a length scale that is difficult to achieve with traditional MD calculations.

Molecular dynamics simulation of laser desorption of a fragment of protein kinase A from two MALDI matrices

We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.

Ion formation mechanisms in UV-MALDI

Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.

Molecular Dynamics Model of Ultraviolet Matrix-Assisted Laser Desorption/Ionization Including Ionization Processes

A molecular dynamics model of UV-MALDI including ionization processes is presented. In addition to the previously described breathing sphere approach developed for simulation of laser ablation/desorption of molecular systems, it includes radiative and nonradiative decay, exciton hopping, two pooling processes, and electron capture. The results confirm the main conclusions of the continuum model of Knochenmuss, Anal. Chem. 2003, 75, 2199, but provide a much more detailed description of the interaction between ablation/desorption and ionization processes in the critical early time regime. Both desorption and ablation regimes generate free ions, and yields are in accordance with experiment. The first molecular ions are emitted at high velocities shortly before neutral desorption begins, because of surface charging caused by electron escape from the top of the sample. Later ions are entrained and thermalized in the plume of neutral molecules and clusters. Clusters are found to be stable on a nanosecond time scale, so the ions in them will be released only slowly, if at all. Exciton hopping rate and the mean radius for ion recombination are shown to be key parameters that can have a significant effect on net ion yield.

Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation

A coarse-grained model has been developed for molecular dynamics simulations of the interaction of light with polymeric materials. The photon energy can result in a vibrational excitation (photothermal process) or disruption of a chemical bond (photochemical process) in a polymer. In the latter case, the formation of active radial sites and the occurrence of chemical reactions have to be taken into consideration. The novel feature of this model is the incorporation of chemical reactions into the united atom approximate representation of the polymer structure, which permits the study of laser ablation, degradation, or the effect of various chemical reactions on large time and length scales. The chemical reactions are included in the model in a probabilistic manner as in the kinetic Monte Carlo method. This model adopts physically and experimentally known quantities such as enthalpies and probabilities of reactions. Properties such as laser irradiation time, laser fluence, and wavelength are explicitly included. Moreover, no chemically correct interaction potential is required to incorporate the effects of chemical reactions on the dynamics of the system after energy deposition. We find that the model provides a plausible description of the essential processes. The laser-induced pressure relaxation is the main mechanism responsible for the onset of polymer ablation. Since the pressure relaxation processes are slow, there is a delay in the onset of ablation after the end of the laser pulse as is observed experimentally. The vaporization processes are not efficient for material removal, and the effect is minimal for both photochemical and photothermal processes. A lower fluence is needed for the onset of ablation with photochemical processes than photothermal processes.