Reconstruction of complex structures is an inverse problem arising in virtually all areas of science and technology, from protein structure determination to bulk heterostructure solar cells and the structure of nanoparticles. We cast this problem as a complex network problem where the edges in a network have weights equal to the Euclidean distance between their endpoints. We present a method for reconstruction of the locations of the nodes of the network given only the edge weights of the Euclidean network. The theoretical foundations of the method are based on rigidity theory, which enables derivation of a polynomial bound on its efficiency. An efficient implementation of the method is discussed and timing results indicate that the run time of the algorithm is polynomial in the number of nodes in the network. We have reconstructed Euclidean networks of about 1000 nodes in approximately 24 h on a desktop computer using this implementation. We also reconstruct Euclidean networks corresponding to polymer chains in two dimensions and planar graphene nanoparticles. We have also modified our base algorithm so that it can successfully solve random point sets when the input data are less precise.

Rabi oscillations typify the inherent nonlinearity of optical excitations in quantum dots. Using an integral kernel formulation to solve the 3D Maxwell-Bloch equations in ensembles of up to 10 4 quantum dots, we observe features in Rabi oscillations due to the interplay of nonlinearity, non-equilibrium excitation, and electromagnetic coupling between the dots. This approach allows us to observe the dynamics of each dot in the ensemble without resorting to spatial averages. Our simulations predict synchronized multiplets of dots that exchange energy, dots that dynamically couple to screen the effect of incident external radiation, localization of the polarization due to randomness and interactions, as well as wavelength-scale regions of enhanced and suppressed polarization.

The chemical modification of amorphous polystyrene (PS) by the deposition of atomic S, SC, and SH with 25, 50, and 100 eV of incident kinetic energy is examined using classical molecular dynamics simulations. The forces are determined using the second-generation reactive empirical bondorder (REBO) potential that has been extended to include sulfur. In all cases, the S atoms or S-containing dimers are deposited randomly on the PS surface with a flux of about 0.4 × 10 24 ions/(cm 2 s), which is comparable to experimental values. The simulations predict the way in which the depth profiles vary as a function of the identity and kinetic energy of the incident atom or dimer. We also quantify the ways in which the surface is chemically modified and provide a profile of the chemical products formed on the surface, within the substrate, or in the material sputtered from the surface. The simulations predict that the maximum density of deposited atoms throughout the surface substrate, 3.32 × 10 18 /cm 3 , occurs for S deposition with 50 eV of incident energy. We further predict that the highest molecular weight products are formed as a result of S deposition with 100 eV of energy. Additionally, the chemical reactions that occur during the deposition are found to depend on the beam energy for all the incident atoms or dimers considered. Negligible change in the surface roughness is predicted to occur as a result of these deposition processes.

No abstract

We propose a computational framework for the self-consistent dynamics of a microsphere system driven by a pulsed acoustic field in an ideal fluid. Our framework combines a molecular dynamics integrator describing the dynamics of the microsphere system with a time-dependent integral equation solver for the acoustic field that makes use of fields represented as surface expansions in spherical harmonic basis functions. The presented approach allows us to describe the interparticle interaction induced by the field as well as the dynamics of trapping in counter-propagating acoustic pulses. The integral equation formulation leads to equations of motion for the microspheres describing the effect of nondissipative drag forces. We show (1) that the field-induced interactions between the microspheres give rise to effective dipolar interactions, with effective dipoles defined by their velocities and (2) that the dominant effect of an ultrasound pulse through a cloud of microspheres gives rise mainly to a translation of the system, though we also observe both expansion and contraction of the cloud determined by the initial system geometry.