Related papers: PHAST: Protein-like heteropolymer analysis by stat…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
Engineering alloys generally exhibit multi-phase microstructures. For simulating their microstructure evolution during solid-state phase transformation, CALPHAD-guided multi-phase-field models coupled with micro-mechanics have proven to be…
A parametric simulation tool for pixel sensors is presented. A realistic pixel response is simulated purely based on measurement input, without requiring detailed knowledge of the underlying manufacturing process. As such, it provides an…
Atomically thin 2-dimensional heterostructures are a promising, novel class of materials with groundbreaking properties. The possiblity of choosing the many constituent components and their proportions allows optimizing these materials to…
This paper presents STrEAM (SuperTrace Evaluation Automated for Matching), a Mathematica package that calculates all functional supertraces which arise when matching a generic UV model onto a relativistic Effective Field Theory (EFT) at one…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
For the self-consistent description of various plasma sources operated in the low-pressure (nonlocal, kinetic) regime, the Particle-In-Cell simulation approach, combined with the Monte Carlo treatment of collision processes (PIC/MCC), has…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
We present here a set of examples, classes and tools which can be used for statistical analysis in Graphics Processing Units (GPU). This includes binned and unbinned maximum likelihood fits, pseudo-experiment generation, convolutions,…
Isothermal and adiabatic shocks, which are produced from fast expansion of the gas, is simulated with smoothed particle hydrodynamics (SPH). The results are compared with the analytic solutions. The algorithm of the program is explained and…
We introduce PyChEst, a Python package which provides tools for the simultaneous estimation of multiple changepoints in the distribution of piece-wise stationary time series. The nonparametric algorithms implemented are provably consistent…
FeTi-based hydrides have recently re-attracted attention as stationary hydrogen storage materials due to favorable reversibility, good sorption kinetics and relatively low costs compared to alternative intermetallic hydrides. Employing the…
Prokaryotic organisms usually possess compact genomes, which are particularly suitable to complete sequencing with existing technologies, which led to an escalating accumulation of available genome data. In response to this ever-expanding…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
The current landscape of scientific research is widely based on modeling and simulation, typically with complexity in the simulation's flow of execution and parameterization properties. Execution flows are not necessarily straightforward…
We discuss in detail a recently proposed hybrid particle-continuum scheme for complex fluids and evaluate it at the example of a confined homopolymer solution in slit geometry. The hybrid scheme treats polymer chains near the impenetrable…
ParaMonte (standing for Parallel Monte Carlo) is a serial and MPI/Coarray-parallelized library of Monte Carlo routines for sampling mathematical objective functions of arbitrary-dimensions, in particular, the posterior distributions of…
We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the…