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As a physical fact, randomness is an inherent and ineliminable aspect in all physical measurements and engineering production. As a consequence, material parameters, serving as input data, are only known in a stochastic sense and thus, also…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
Like other engineering disciplines, software engineering should also have principles to guide the construction of sustainable computer applications. Tangible properties include a) unlimited scalability, b) maximal reproducibility, and c)…
Machine learning models are changing the paradigm of molecular modeling, which is a fundamental tool for material science, chemistry, and computational biology. Of particular interest is the inter-atomic potential energy surface (PES). Here…
One of the key challenges in sensor networks is the extraction of information by fusing data from a multitude of distinct, but possibly unreliable sensors. Recovering information from the maximum number of dependable sensors while…
In the context of the recently developed "equation-free" approach to the computer-assisted analysis of complex systems, we illustrate the computation of coarsely self-similar solutions. Dynamic renormalization and fixed point algorithms for…
Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents…
The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they…
Modeling complex spatiotemporal dynamical systems, such as the reaction-diffusion processes, have largely relied on partial differential equations (PDEs). However, due to insufficient prior knowledge on some under-explored dynamical…
The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the…
Software Engineering practitioners work using highly diverse methods and practices, and general theories in software engineering are lacking. One attempt at creating a common ground in the area of software engineering methodologies has been…
The design of structural & functional materials for specialized applications is being fueled by rapid advancements in materials synthesis, characterization, manufacturing, with sophisticated computational materials modeling frameworks that…
We introduce a new code, ECOSMOG, to run N-body simulations for a wide class of modified gravity and dynamical dark energy theories. These theories generally have one or more new dynamical degrees of freedom, the dynamics of which are…
Soft material research has seen significant growth in recent years, with emerging applications in robotics, electronics, and healthcare diagnostics where understanding material mechanical response is crucial for precision design.…
Argon molecular dynamics (MD) simulations are performed with a newly developed MD program, Easy M(1)odular M(2)olecular M(3)echanics (EM3). The program was developed in an object-oriented fashion containing classes for each critical part of…
Monte Carlo (MC) simulations are powerful computational tools for investigating thermodynamic behavior and validating analytical approaches in complex physical systems. Here we present ETHER (Efficient Tool for THermodynamics Exploration…
From understanding the sand on the beach to the foam on your beer, soft sphere simulations have been crucial to the study of the amorphous world around us. However, many of the materials we interact with on a daily basis aren't comprised of…
We present the SLIM (https://github.com/slimgroup) open-source software framework for computational geophysics, and more generally, inverse problems based on the wave-equation (e.g., medical ultrasound). We developed a software environment…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Most methods for estimating configurational entropy from molecular simulation data yield upper limits except for harmonic systems where they are exact. Problems arise at diffusive systems and the presence of conformational transitions.…