Molecular Dynamics Simulation of Dipalmitoylphosphatidylserine Bilayer with Na+ Counterions

AbstractWe performed a molecular dynamics simulation of dipalmitoylphosphatidylserine (DPPS) bilayer with Na+ counterions. We found that hydrogen bonding between the NH3+ group and the phosphate group leads to a reduction in the area per headgroup when compared to the area in dipalmitoylphosphatidylcholine bilayer. The Na+ ions bind to the oxygen in the carboxyl group of serine, thus giving rise to a dipolar bilayer similar to dipalmitoylphosphatidylethanolamine bilayer. The results of the simulation show that counterions play a crucial role in determining the structural and electrostatic properties of DPPS bilayer

Effect of shape anisotropy on transport in a 2-dimensional computational model: Numerical simulations showing experimental features observed in biomembranes

We propose a 2-d computational model-system comprising a mixture of spheres and the objects of some other shapes, interacting via the Lennard-Jones potential. We propose a reliable and efficient numerical algorithm to obtain void statistics. The void distribution, in turn, determines the selective permeability across the system and bears a remarkable similarity with features reported in certain biological experiments.Comment: 1 tex file, 2 sty files and 5 figures. To appear in Proc. of StatPhys conference held in Calcutta, Physica A 199

Random spread on the family of small-world networks

We present the analytical and numerical results of a random walk on the family of small-world graphs. The average access time shows a crossover from the regular to random behavior with increasing distance from the starting point of the random walk. We introduce an {\em independent step approximation}, which enables us to obtain analytic results for the average access time. We observe a scaling relation for the average access time in the degree of the nodes. The behavior of average access time as a function of $p$, shows striking similarity with that of the {\em characteristic length} of the graph. This observation may have important applications in routing and switching in networks with large number of nodes.Comment: RevTeX4 file with 6 figure

DCMS: A data analytics and management system for molecular simulation

Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface (i.e., SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression

Transferable interactions of Li+ and Mg2+ ions in polarizable models

Therapeutic implications of Li(+), in many cases, stem from its ability to inhibit certain Mg(2+)-dependent enzymes, where it interacts with or substitutes for Mg(2+). The underlying details of its action are, however, unknown. Molecular simulations can provide insights, but their reliability depends on how well they describe relative interactions of Li(+) and Mg(2+) with water and other biochemical groups. Here, we explore, benchmark, and recommend improvements to two simulation approaches: the one that employs an all-atom polarizable molecular mechanics (MM) model and the other that uses a hybrid quantum and MM implementation of the quasi-chemical theory (QCT). The strength of the former is that it describes thermal motions explicitly and that of the latter is that it derives local contributions from electron densities. Reference data are taken from the experiment, and also obtained systematically from CCSD(T) theory, followed by a benchmarked vdW-inclusive density functional theory. We find that the QCT model predicts relative hydration energies and structures in agreement with the experiment and without the need for additional parameterization. This implies that accurate descriptions of local interactions are essential. Consistent with this observation, recalibration of local interactions in the MM model, which reduces errors from 10.0 kcal/mol to 1.4 kcal/mol, also fixes aqueous phase properties. Finally, we show that ion–ligand transferability errors in the MM model can be reduced significantly from 10.3 kcal/mol to 1.2 kcal/mol by correcting the ligand’s polarization term and by introducing Lennard-Jones cross-terms. In general, this work sets up systematic approaches to evaluate and improve molecular models of ions binding to proteins