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Intrinsically disordered proteins (IDPs) play a significant role in intracellular phenomena and are known to exist in an ensemble of inter-converting conformations in solution. Accurately modeling the conformations of IDPs in solution poses…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Water is an important molecule in the chemical and thermal balance of dense molecular gas, but knowing its history through-out the various stages of the star formation is a fundamental problem. Its molecular deuteration provides us with a…
Water is a complex structured liquid of hydrogen-bonded molecules that displays a surprising array of unusual properties, also known as water anomalies, the most famous being the density maximum at about $4^\circ$C. The origin of these…
Heterostructures of 2D materials offer a fertile ground to study ion transport and charge storage. Here we employ ab initio molecular dynamics to examine the proton-transfer/diffusion and redox behavior in a water layer confined in the…
The quality and ease of proteomics analysis depends on the performance of the analytical tools used, and thus of the performances of the protein separation tools used to deconvolute complex protein samples. Among protein samples, membrane…
In contrast to the well-known destabilization of globular proteins by high pressure, re- cent work has shown that pressure stabilizes the formation of isolated {\alpha}-helices. However all simulations to date have obtained a qualitatively…
Simplified, classical models of water are an integral part of atomistic molecular simulations, especially in biology and chemistry where hydration effects are critical. Yet, despite several decades of effort, these models are still far from…
Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR…
Infrared (IR) absorption in the 1000-3700 cm-1 range and 1H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H7+O3, in acetonitrile. The core H7+O3 motif persists in larger protonated water clusters in…
Aqueous solutions of HF and HCl behave very differently at intermediate concentrations: HCl dissociates completely, whereas HF remains only partially dissociated and forms bifluoride (HF$_2^-$). This should lead to different excess-proton…
Mon R2, at a distance of 830 pc, is the only ultracompact HII region (UC HII) where the photon-dominated region (PDR) between the ionized gas and the molecular cloud can be resolved with Herschel. HIFI observations of the abundant compounds…
The efficiency of a proton exchange membrane (PEM) fuel cell depends on the mobility of protons in the PEM, which is determined by the hydration and temperature of the membrane. While optical techniques or neutron or x-ray scattering…
We have investigated the dynamics of liquid water confined in mesostructured porous silica (MCM-41) and periodic mesoporous organosilicas (PMOs) by incoherent quasielastic neutron scattering experiments. The effect of tuning the…
Hydrogels which are hydrophilic and porous materials have recently emerged as promising systems for filtration applications. In our study, we prepare hydrogel membranes by the photopolymerization of a mixture of poly (ethylene glycol)…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
Within the frame of an effective, coarse-grained hydrophobic-polar protein model, we employ multicanonical Monte Carlo simulations to investigate free-energy landscapes and folding channels of exemplified heteropolymer sequences, which are…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…