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This paper considers the arbitrary-proportional finite-set-partitioning problem which involves partitioning a finite set into multiple subsets with respect to arbitrary nonnegative proportions. This is the core art of many fundamental…
Polymer conformation generation is a critical task that enables atomic-level studies of diverse polymer materials. While significant advances have been made in designing conformation generation methods for small molecules and proteins,…
A geometric numerical method for simulating suspensions of spherical and non-spherical particles with Stokes drag is proposed. The method combines divergence-free matrix-valued radial basis function interpolation of the fluid velocity field…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
The plastic flow of a polycrystal is analyzed assuming grains as fine that the rate limiting process is grain boundary sliding, and grains readily accommodate their shapes by slip to preserve spatial continuity. It is shown that thinking of…
Forward-flux sampling (FFS) is a path sampling technique that has gained increased popularity in recent years, and has been used to compute rates of rare event phenomena such as crystallization, condensation, hydrophobic evaporation, DNA…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
Matching promises transparent causal inferences for observational data, making it an intuitive approach for many applications. In practice, however, standard matching methods often perform poorly compared to modern approaches such as…
The feedback particle filter (FPF) is an innovative, control-oriented and resampling-free adaptation of the traditional particle filter (PF). In the FPF, individual particles are regulated via a feedback gain, and the corresponding gain…
Recently, it has been shown that entropy can be used to sort Brownian particles according to their size. In particular, a combination of a static and a time-dependent force applied on differently sized particles which are confined in an…
The COVID-19 pandemic has caused a global shortage of personal protective equipment. While existing supply chains are struggling to meet the surge in demand, the limited supply of N95 filtering facepiece respirators (FFRs) has placed…
The collision dynamics of hard spheres and cylindrical pores is solved exactly, which is the minimal model for a regularly porous membrane. Nonequilibrium event-driven molecular dynamics simulations are used to show that the permeability…
Genome sequencing projects are rapidly increasing the number of high-dimensional protein sequence datasets. Clustering a high-dimensional protein sequence dataset using traditional machine learning approaches poses many challenges. Many…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
Dissipative particle dynamics is a widely used mesoscale technique for the simulation of hydrodynamics (as well as immersed particles) utilizing coarse-grained molecular dynamics. While the method is capable of describing any fluid, the…
Polymer chains dissolved in a solvent take random conformations due to large internal degrees of freedom and are characterized geometrically by their average shape and size. The diffusive dynamics of such large macromolecules play an…
The Cellular Potts Model (CPM) is a lattice based modeling technique which is widely used for simulating cellular patterns such as foams or biological tissues. Despite its realism and generality, the standard Monte Carlo algorithm used in…
Using molecular dynamic simulation, we study the stretching of an adsorbed homopolymer in a poor solvent with one end held at a distance $z_e$ from the substrate. We measure the vertical force $f$ on the end of the chain as a function of…
This work investigates the migration of spherical particles of different sizes in a centrifuge-driven deterministic lateral displacement (c-DLD) device. Specifically, we use a scaled-up model to study the motion of suspended particles…
Solutions of semiflexible polymers confined by repulsive planar walls are studied by density functional theory and Molecular Dynamics simulations, to clarify the competition between the chain alignment favored by the wall and the depletion…