Jayendran C. Rasaiah

Bio: Jayendran C. Rasaiah is an academic researcher from University of Maine. The author has contributed to research in topics: Ion & Solvation. The author has an hindex of 36, co-authored 86 publications receiving 8854 citations. Previous affiliations of Jayendran C. Rasaiah include National Institutes of Health & State University of New York System.

Water conduction through the hydrophobic channel of a carbon nanotube

Abstract: Confinement of matter on the nanometre scale can induce phase transitions not seen in bulk systems1. In the case of water, so-called drying transitions occur on this scale2,3,4,5 as a result of strong hydrogen-bonding between water molecules, which can cause the liquid to recede from nonpolar surfaces to form a vapour layer separating the bulk phase from the surface6. Here we report molecular dynamics simulations showing spontaneous and continuous filling of a nonpolar carbon nanotube with a one-dimensionally ordered chain of water molecules. Although the molecules forming the chain are in chemical and thermal equilibrium with the surrounding bath, we observe pulse-like transmission of water through the nanotube. These transmission bursts result from the tight hydrogen-bonding network inside the tube, which ensures that density fluctuations in the surrounding bath lead to concerted and rapid motion along the tube axis7,8,9. We also find that a minute reduction in the attraction between the tube wall and water dramatically affects pore hydration, leading to sharp, two-state transitions between empty and filled states on a nanosecond timescale. These observations suggest that carbon nanotubes, with their rigid nonpolar structures10,11, might be exploited as unique molecular channels for water and protons, with the channel occupancy and conductivity tunable by changes in the local channel polarity and solvent conditions.

Solvent Structure, Dynamics, and Ion Mobility in Aqueous Solutions at 25 °C

Abstract: We calculate the mobilities ui of the metal cations Li+, Na+, K+, Rb+, Cs+, and Ca2+ and the halides F-, Cl-, Br-, and I- at infinite dilution by molecular dynamics simulation using the SPC/E model for water at 25 °C and a reaction field for the long-range interactions. The ion mobilities show the same trends as the experimental results with distinct maxima for cations and anions. The mobilities (defined by ui = Di/kT) of the corresponding uncharged species are also determined by simulation and are in qualitative agreement with Stokes' law. The mobilities of Li+, Na+, K+, Rb+ and F- increase on discharge, whereas Cl, Br, and I have smaller mobilities than the corresponding anions. The mobility of the fictitious I+ ion, which differs from I- only in its charge, lies between that of I- and I in the order uI < uI+ < uI−. The residence time of water in the first solvation shell of small cations (Li+ and Na+) and Ca2+ decreases when the ions are discharged, while the opposite is observed on neutralizing I-, su...

Water in Nonpolar Confinement: From Nanotubes to Proteins and Beyond *

Abstract: Water molecules confined to nonpolar pores and cavities of nanoscopic dimensions exhibit highly unusual properties. Water filling is strongly cooperative, with the possible coexistence of filled and empty states and sensitivity to small perturbations of the pore polarity and solvent conditions. Confined water molecules form tightly hydrogen-bonded wires or clusters. The weak attractions to the confining wall, combined with strong interactions between water molecules, permit exceptionally rapid water flow, exceeding expectations from macroscopic hydrodynamics by several orders of magnitude. The proton mobility along 1D water wires also substantially exceeds that in the bulk. Proteins appear to exploit these unusual properties of confined water in their biological function (e.g., to ensure rapid water flow in aquaporins or to gate proton flow in proton pumps and enzymes). The unusual properties of water in nonpolar confinement are also relevant to the design of novel nanofluidic and molecular separation devices or fuel cells.

Molecular Dynamics Simulation of Ion Mobility. 2. Alkali Metal and Halide Ions Using the SPC/E Model for Water at 25 °C†

Abstract: We present results of computer simulations of the mobilities of the alkali metal ions (Li+, Na+, K+, Rb+, and Cs+) and the halides (F-, Cl-, Br-, and I-) at 25 °C using the SPC/E model for water and ion−water parameters fitted to the binding energies of small clusters of ions. A simple truncation of the ion−water and water−water potentials was used, and the mobilities calculated from the mean square displacement and the velocity autocorrelation functions, respectively, were found to be in good agreement with each other. The calculations demonstrate, for the first time, cation and anion mobilities that fall on separate curves, as functions of ion size, with distinct maxima. This is in complete accord with experimental trends observed in water at 25 °C. The cation mobilities are also in better agreement with the measured values than the calculations done earlier (J. Chem. Phys. 1994, 101, 6964) using the TIP4P model. The mobilities of the halides calculated here for the SPC/E model are however slightly lowe...

Thermodynamic perturbation theory for simple polar fluids. II

Abstract: The study of polar fluids begun in a previous paper is continued. Calculations for the Stockmayer potential are extended to include the term of order μ6, where μ is the dipole moment. The effects of higher-order terms are then approximated by means of a simple Pade extrapolation procedure, and the liquid-gas coexistence curve is located in this approximation. An orientation-independent but temperature-dependent potential that is thermodynamically equivalent to an arbitrary orientation-dependent potential is introduced and used to assess the lowest-order thermodynamic effects that result from the presence of quadrupole and octupole terms in the pair-potential. Several values of quadrupole and octupole moments representative of a dipolar molecule (HCl) as well as linear molecules (N2, O2 and CO2, for which μ=0) are considered.

Scalable molecular dynamics with NAMD

Abstract: NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

Science and technology for water purification in the coming decades

Abstract: One of the most pervasive problems afflicting people throughout the world is inadequate access to clean water and sanitation. Problems with water are expected to grow worse in the coming decades, with water scarcity occurring globally, even in regions currently considered water-rich. Addressing these problems calls out for a tremendous amount of research to be conducted to identify robust new methods of purifying water at lower cost and with less energy, while at the same time minimizing the use of chemicals and impact on the environment. Here we highlight some of the science and technology being developed to improve the disinfection and decontamination of water, as well as efforts to increase water supplies through the safe re-use of wastewater and efficient desalination of sea and brackish water.

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy.

Abstract: Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms Docking accuracy is assessed by redocking ligands from 282 cocrystallized PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose Errors in geometry for the top-ranked pose are less than 1 A in nearly ha

Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes

Abstract: A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motifs leading to enhanced binding affinity are included: (1) hydrophobic enclosure where groups of lipophilic ligand atoms are enclosed on opposite faces by lipophilic protein atoms, (2) neutral-neutral single or correlated hydrogen bonds in a hydrophobically enclosed environment, and (3) five categories of charged-charged hydrogen bonds. The XP scoring function and docking protocol have been developed to reproduce experimental binding affinities for a set of 198 complexes (RMSDs of 2.26 and 1.73 kcal/mol over all and well-docked ligands, respectively) and to yield quality enrichments for a set of fifteen screens of pharmaceutical importance. Enrichment results demonstrate the importance of the novel XP molecular recognition and water scoring in separating active and inactive ligands and avoiding false positives.