Related papers: Off-lattice simulation of the solid phase DNA ampl…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
Using lattice overlap fermions, we have computed the 1-loop renormalization factors of several operators that measure DIS structure functions and weak amplitudes. Computer codes written in the algebraic manipulation language FORM have been…
We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
Particle-based simulations are performed to study the post-relaxation dynamics of functionalized (patchy) colloids adsorbed on an attractive substrate. Kinetically arrested structures that depend on the number of adsorbed particles and the…
Silicon photonics in conjunction with complementary metal-oxide-semiconductor (CMOS) fabrication has greatly enhanced the development of integrated optical phased arrays. This facilitates a dynamic control of light in a compact form factor…
We present a new quantum-limited Josephson-junction-based 3-wave-mixing parametric amplifier, the SNAIL Parametric Amplifier (SPA), which uses an array of SNAILs (Superconducting Nonlinear Asymmetric Inductive eLements) as the source of…
Supported Lipid Bilayers (SLBs) are model membranes formed at solid substrate surfaces. This architecture renders the membrane experimentally accessible to surface sensitive techniques used to study their properties, including Atomic Force…
The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in…
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics…
We investigate the localization observed recently for locally non-hermitian Hamiltonians by studying the effect of the amplification on the scaling behavior of the transmission and reflection phases in 1D periodic chains of…
Surrogate models for computational simulations are input-output approximations that allow computationally intensive analyses, such as uncertainty propagation and inference, to be performed efficiently. When a simulation output does not…
Superconducting Parametric Amplifiers (SPAs) have seen great interest in recent years due to their high gain and quantum limited noise performance. Among these amplifiers, resonant SPAs have been widely developed for experiments where ultra…
Simulations with 2+1 flavors of domain wall fermions provide us with the opportunity to compare the lattice data directly to the predictions of continuum chiral perturbation theory, up to corrections from the residual chiral symmetry…
A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous…
DNA adsorption on solid or liquid surfaces is a topic of broad fundamental and applied interest. Here we study by x-ray reflectivity the adsorption of monodisperse double-stranded DNA molecules a positively-charged surface, obtained through…
We discuss the decay of a two-level system into an engineered reservoir of coupled harmonic oscillators in the single-excitation manifold and propose its optical simulation with an homogeneous chain of coupled waveguides where individual…
Over the last decades, theoretical photochemistry has produced multiple techniques to simulate the nonadiabatic dynamics of molecules. Surprisingly, much less effort has been devoted to adequately describing the first step of a…
We study the scalar condensate and the topological susceptibility for a continuous range of quark masses in the Schwinger model with $N_f=0,1,2$ dynamical flavors, using both the overlap and the staggered discretization. At finite lattice…
We propose an algorithm using a modified variant of amplitude amplification to solve combinatorial optimization problems via the use of a subdivided phase oracle. Instead of dividing input states into two groups and shifting the phase…
ZSPA-1 is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed ZSPA-1 shows a reduced helix content and a melting behavior that is less cooperative, compared with the…