arXiv subjects

Ali Hassanali

Publications and source records attributed to Ali Hassanali.

41 records · Page 3Linked to original sources

arXiv2021

Learning the Hydrophilic, Hydrophobic and Aromatic Character of Amino Acids from their Interfacial Thermal Conductance in Water

In this study, the thermal relaxation of the 20 naturally occurring amino-acids in water is investigated using transient non-equilibrium molecular-dynamics simulations. By modeling the thermal relaxation process, the relaxation times of the amino-acids in water occurs over a timescale covering 2-5 ps. For the hydrophobic amino acids, the relaxation time is controlled by the size of the hydrocarbon side chain, while for hydrophilic amino acids, the number of hydrogen bonds do not significantly affect the timescales of the heat dissipation. Our results show that the interfacial thermal conductance at the amino-acid water interface is in the range of~40-80 MWm$^{-2}$K$^{-1}$. Hydrophobic and aromatic amino acids tend to have a lower interfacial thermal conductance. Notably, we reveal that amino acids can be classified, in terms of their thermal relaxation times and molar masses, into simply connected phases with the same hydrophilicity, hydrophibicity and aromaticity.

cond-mat.soft↗

arXiv2020

Structural and Dynamical Fingerprints of the Anomalous Dielectric Properties of Water Under Confinement

There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the dielectric, structural and dynamical properties of confined water placed between two parallel graphene walls at different inter distances from the Angstrom scale to few tens of nanometer have been investigated using molecular dynamics. For dielectric properties of water, we show that the perpendicular component of water dielectric constant drastically decreases under sub $2\; nm$ spatial confinement. The achieved dielectric constant data through linear response and fluctuation-dissipation theory, are consistent with recent reported experimental results. By determining the charge density as well as fluctuations in the number of atoms, we provide a molecular rationale for the behavior of perpendicular dielectric response function. We also interpret the behavior of the dielectric response in terms of the presence of dangling O-H bonds of waters. By examining the residence time and lateral diffusion constant of water under confinement, we reveal that the water molecules tend to keep their hydrogen bond networks at the interface of water-graphene. We also found consistency between lateral diffusion and z-component of variance in the center of mass of the system as a function of confinement.

cond-mat.stat-mech↗

arXiv2020

First-passage Fingerprints of Water Diffusion near Glutamine Surfaces

The extent to which biological interfaces affect the dynamics of water plays a key role in the exchange of matter and chemical interactions that are essential for life. The density and the mobility of water molecules depend on their proximity to biological interfaces and can play an important role in processes such as protein folding and aggregation. In this work, we study the dynamics of water near glutamine surfaces---a system of interest in studies of neurodegenerative diseases. Combining molecular-dynamics simulations and stochastic modelling, we study how the mean first-passage time and related statistics of water molecules escaping subnanometer-sized regions vary from the interface to the bulk. Our analysis reveals a dynamical complexity that reflects underlying chemical and geometrical properties of the glutamine surfaces. From the first-passage time statistics of water molecules, we infer their space-dependent diffusion coefficient in directions normal to the surfaces. Interestingly, our results suggest that the mobility of water varies over a longer length scale than the chemical potential associated with the water-protein interactions. The synergy of molecular dynamics and first-passage techniques opens the possibility for extracting space-dependent diffusion coefficients in more complex, inhomogeneous environments that are commonplace in living matter.

cond-mat.stat-mech↗

arXiv2019

Charge Transfer as a Ubiquitous Mechanism in Determining the Negative Charge at Hydrophobic Interfaces

The origin of the apparent negative charge at hydrophobic-water interfaces has fueled one of the biggest debates in physical chemistry for several decades. The most common interpretation given to explain this observation is that negatively charged hydroxide ions (OH-) bind strongly to the interfaces. Here, using first principles calculations of the air-water and oil-water interfaces consisting of thousands of atoms, we unravel a mechanism that does not require the presence of OH-. We show that small amounts of charge transfer along hydrogen bonds and asymmetries in the hydrogen bond network, associated with local topological defects can lead to the accumulation of negative surface charge at both interfaces. For water near oil, we show that there is also some spillage of electron density into the oil leaving it negatively charged. The surface charge densities at both interfaces is computed to be approximately $-0.015$ e/nm$^{2}$ in agreement with electrophoretic experiments. We also show, using an energy decomposition analysis, that the electronic origin of this phenomena is rooted in a collective polarization and charge transfer effect.

physics.chem-ph↗

arXiv2019

Thermal transport at a nanoparticle-water interface: A molecular dynamics and continuum modeling study

Heat transfer between a silver nanoparticle and surrounding water has been studied using molecular dynamics (MD) simulations. The thermal conductance (Kapitza conductance) at the interface between a nanoparticle and surrounding water has been calculated using four different approaches: transient with/without temperature gradient (internal thermal resistance) in the nanoparticle, steady-state non-equilibrium and finally equilibrium simulations. The results of steady-state non-equilibrium and equilibrium are in agreement but differ from the transient approach results. MD simulations results also reveal that in the quenching process of a hot silver nanoparticle, heat dissipates into the solvent over a length-scale of ~ 2nm and over a timescale of less than 5ps. By introducing a continuum solid-like model and considering a heat conduction mechanism in water, it is observed that the results of the temperature distribution for water shells around the nanoparticle agree well with MD results. It is also found that the local water thermal conductivity around the nanoparticle is greater by about 50 percent than that of bulk water. These results have important implications for understanding heat transfer mechanisms in nanofluids systems and also for cancer photothermal therapy, wherein an accurate local description of heat transfer in an aqueous environment is crucial.

cond-mat.mtrl-sci↗