Related papers: Diffusion NMR study of complex formation in membra…
A numerical method based on smoothed particle hydrodynamics with adaptive spatial resolution (SPH-ASR) was developed for simulating free surface flows. This method can reduce the computational demands while maintaining the numerical…
Semi-permeable membranes are important elements in water purification and energy generation applications, for which the atomic thickness and strength of graphene can enhance efficiency and permeation rate while maintaining good selectivity.…
We present a dissipative particle dynamics (DPD) simulation study on the surface modification of initiator embedded microparticles (MPs) of different shapes via atom transfer radical polymerization (ATRP) brush growth. The surface-initiated…
Motivation: Microarray experiments result in large scale data sets that require extensive mining and refining to extract useful information. We have been developing an efficient novel algorithm for nonmetric multidimensional scaling (nMDS)…
We develop a computational method based on Dissipative Particle Dynamics (DPD) that introduces solvent hydrodynamic interactions to coarse-grained models of solutes, such as ions, molecules, or polymers. DPD-solvent (DPDS) is a fully…
Liquid-phase exfoliation of two-dimensional materials is very attractive for large-scale applications. Although used extensively, isolating MoS2 layers (<10) with high efficiency is reported to be extremely difficult. Further, the…
A phenomenological macroscopic model of the Giant Dipole Resonance (GDR) damping width of cold- and hot-nuclei with ground-state spherical and near-spherical shapes is developed. The model is based on a generalized Fermi Liquid model which…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Pebble accretion offers an efficient pathway to form planets, driven by a constant supply of inward drifting mass and an accretion efficiency enhanced by gas drag. While most studies assume a single pebble size (monodisperse), real discs…
Combining microfluidic devices with nuclear magnetic resonance (NMR) has the potential of unlocking their vast sample handling and processing operation space for use with the powerful analytics provided by NMR. One particularly challenging…
De novo peptide sequencing aims to recover amino acid sequences of a peptide from tandem mass spectrometry (MS) data. Existing approaches for de novo analysis enumerate MS evidence for all amino acid classes during inference. It leads to…
We have revisited the composition dependence of principal properties of liquid water-DMSO mixtures by using the isobaric-isothermal molecular dynamics computer simulations. A set of non-polarizable semi-flexible models for the DMSO molecule…
Nanomechanical spectroscopy (NMS) is a recently developed approach to determine optical absorption spectra of nanoscale materials via mechanical measurements. It is based on measuring changes in the resonance frequency of a membrane…
Even though compressible plasma turbulence is encountered in many astrophysical phenomena, its effect is often not well understood. Furthermore, direct numerical simulations are typically not able to reach the extreme parameters of these…
The gradient discretisation method (GDM) is a generic framework for designing and analysing numerical schemes for diffusion models. In this paper, we study the GDM for the porous medium equation, including fast diffusion and slow diffusion…
The giant dipole resonance's (GDR) width and shape at finite temperature and angular momentum are described within the phonon damping model (PDM), which predicts an overall increase in the GDR's total width at low and moderate temperature…
Therapeutic peptides represent a unique class of pharmaceutical agents crucial for the treatment of human diseases. Recently, deep generative models have exhibited remarkable potential for generating therapeutic peptides, but they only…
The strength functions of giant dipole resonance (GDR) in oxygen $^{18 - 24}$O, calcium $^{50 - 60}$Ca, and tin $^{120 - 130}$Sn isotopes are calculated within the phonon damping model under three approximations: without superfluid pairing,…
We have studied the composition dependence of density of liquid water-DMSO mixtures at different temperatures by using the isobaric-isothermal (NPT) molecular dynamics computer simulations. The non-polarizable semi-flexible, P1 and P2…
Numerical methods are proposed for an advanced Poisson-Nernst-Planck-Fermi (PNPF) model for studying ion transport through biological ion channels. PNPF contains many more correlations than most models and simulations of channels, because…