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There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Aerosol injectors applied in single-particle diffractive imaging experiments demonstrated their potential in efficiently delivering nanoparticles with high density. Continuous optimization of injector design is crucial for achieving…
We developed a portable code for dissipative particle dynamics (DPD) simulations. This Fortran program named CAMUS has a couple of notable features. One is the omission of constructing the so-called neighboring particles list, providing a…
We compare experimental data and numerical simulations for the dynamics of inertial particles with finite density in turbulence. In the experiment, bubbles and solid particles are optically tracked in a turbulent flow of water using an…
Molecular simulations are essential tools in computational chemistry, enabling the prediction and understanding of molecular interactions and thermodynamic properties of biomolecules. However, traditional force fields face significant…
Density profiles are the most common measure of inhomogeneous structure in confined fluids, but their connection to transport coefficients is poorly understood. We explore via simulation how tuning particle-wall interactions to flatten or…
We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…
This note presents a simulation method for investigating the relationship between porosity and particle size distribution in porous media characterization. The method simulates particle packing based on particle size distributions,…
The Transfer Matrix Method (TMM) has become a prominent tool for the optical simulation of thin$-$film solar cells, particularly among researchers specializing in organic semiconductors and perovskite materials. As the commercial viability…
PolyMAPS is an open-source library that helps researchers to initialize LAMMPS molecular dynamics simulations. It introduces an integrated workflow by combining preparation, launching, visualization, and analysis into a single Jupyter…
High-throughput approximations of quantum mechanics calculations and combinatorial experiments have been traditionally used to reduce the search space of possible molecules, drugs and materials. However, the interplay of structural and…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Given an algorithm the quality of the output largely depends on a proper specification of the input parameters. A lot of work has been done to analyze tasks related to using a fixed model [25] and finding a good set of inputs. In this paper…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
A computer simulation model is used to study the density profile and flow of a miscible gaseous fluid mixture consisting of differing constituent masses ($m_A = m_B/3$) through an open matrix. The density profile is found to decay with the…
Determining the physicochemical properties of a protein can reveal important insights in their structure, biological functions, stability, and interactions with other molecules. Although tools for computing properties of proteins already…