Related papers: Electrostatic Binding and Hydrophobic Collapse of …
We present a generic model to describe the fractal self-assembly of proteins in terms of electrostatic and hydrophobic interactions. The predictions of the model were correlated with the simulated fractals obtained using patchy…
Binding of Pheophorbide-a of to poly-L-lysine (PLL) have been studied in neutral aqueous buffered solutions of low and near-physiological ionic strengths with low ethanol content (2.4-5.9 %) a wide range of molar polymer-to-dye ratios (P/D)…
Depletion forces play a role in the compaction and de-compation of chromosomal material in simple cells but it remains debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics…
The hydrophobic-polar (HP) model represents proteins as binary strings embedded in lattices, with fold quality measured by an energy score. We prove that the optimal fold energy is not monotonic under concatenation for several standard…
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study aggregation of short peptides in a coarse-grained model with…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
We study colloidal particles in a nematic-liquid-crystal-filled microfluidic channel and show how elastic interactions between the particle and the channel wall lead to different particle dynamics compared with conventional microfluidics.…
Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising…
Catalytically active colloids maintain non-equilibrium conditions in which they produce and deplete chemicals and hence effectively act as sources and sinks of molecules. While individual colloids that are symmetrically coated do not…
Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity…
Active colloids belong to a class of non-equilibrium systems where energy uptake, conversion and dissipation occurs at the level of individual colloidal particles, which can lead to particles self-propelled motion and surprising collective…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
In this paper, we theoretically study the electrostatic interaction between a pair of identical colloids with constant surface potentials sitting in close vicinity of each other at a fluid interface. By employing a simplified yet reasonable…
The design of large-scale colloidal quantum dots (QDs) assemblies and the investigation of their interaction with their close environment are of great interest for improving QD-based optoelectronic devices' performances. Understanding the…
We present a set of molecular dynamics (MD) simulations of strongly charged, flexible polyelectrolyte chains under poor solvent conditions in a salt free solution. Structural properties of the chains and of the solutions are reported. By…
The distance dependence and atomic-scale contrast observed in nominal contact potential difference (CPD) signals recorded by KPFM on surfaces of insulating and semiconducting samples, have stimulated theoretical attempts to explain such…
We report how the electron transport through a solid-state metal/Gly-Gly-His tripeptide (GGH) monolayer/metal junction and the metal/GGH work function are modified by the GGH complexation with Cu2+ ions. Conducting AFM is used to measure…
We present a probabilistic approach to water-water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a hydrophobic particle and hydrophobe…
Among the unsolved problems in computational biology, protein folding is one of the most interesting challenges. To study this folding, tools like neural networks and genetic algorithms have received a lot of attention, mainly due to the…
The ENUF method, i.e., Ewald summation based on the Non-Uniform FFT technique (NFFT), is implemented in Dissipative Particle Dynamics (DPD) simulation scheme to fast and accurately calculate the electrostatic interactions at mesoscopic…