Ulrich Essmann

Bio: Ulrich Essmann is an academic researcher from University of North Carolina at Chapel Hill. The author has contributed to research in topics: Spinodal & Phase diagram. The author has an hindex of 17, co-authored 19 publications receiving 18285 citations. Previous affiliations of Ulrich Essmann include Sapienza University of Rome & Boston University.

A smooth particle mesh Ewald method

Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

Phase behaviour of metastable water

Abstract: THE metastable extension of the phase diagram of liquid water exhibits rich features that manifest themselves in the equilibrium properties of water. For example, the density maximum at 4 °C and the minimum in the isothermal compressibility at 46 °C are thought to reflect the presence of singularities in the behaviour of thermodynamic quantities occurring in the supercooled region1 2. The 'stability–limit conjecture'3–5 suggests that these thermodynamic anomalies arise from a single limit of mechanical stability (spinodal line), originating at the liquid–gas critical point, which determines the limit of both superheating at high temperatures and supercooling at low temperatures. Here we present a comprehensive series of molecular dynamics simulations which suggest that, instead, the supercooling anomalies are caused by a newly identified critical point, above which the two metastable amorphous phases of ice (previously shown to be separated by a line of first-order transitions6,7) become indistinguishable. The two amorphous ice phases are thus incorporated into our understanding of the liquid state, providing a more complete picture of the metastable and stable behaviour of water.

Line of compressibility maxima in the phase diagram of supercooled water

Abstract: We evaluate thermodynamic, structural, and transport properties from extensive molecular-dynamics computer simulations of the ST2 and TIP4P models of liquid water over a wide range of thermodynamic states. We find a line in the phase diagram along which the isothermal compressibility of the supercooled liquid is a maximum. We further observe that along this line the magnitude of the maximum increases with decreasing temperature. Extrapolation to temperatures below those we are able to simulate suggests that the compressibility diverges. In this case, the line of compressibility maxima develops into a critical point followed at lower temperature by a line of first-order phase transitions. The behavior of structural and transport properties of simulated water supports the possibility of a line of first-order phase transitions separating two liquid phases differing in density. We therefore examine the experimentally known properties of liquid and amorphous solid water to test if the equation of state of the liquid might exhibit a line of compressibility maxima, possibly connected to a critical point that is the terminus of a line of phase transitions. We find that the currently available experimental data are consistent with these possibilities. @S1063-651X~97!09501-9#

Simulation of Sodium Dodecyl Sulfate at the Water−Vapor and Water−Carbon Tetrachloride Interfaces at Low Surface Coverage

Abstract: To study the effect of the interface on the properties of an anionic surfactant molecule, sodium dodecyl sulfate (SDS), we performed two molecular dynamics computer simulations. In one simulation, the behavior of SDS at the water−vapor interface was examined. In parallel, we performed a simulation with the molecule embedded at the water−CCl4 interface. A substantial difference in the configurational properties of the amphiphile was observed. At the water−vapor interface, the solute in its most probable configuration was bent, giving rise to two domains within the molecule: the first, containing the head group and several methyl groups, was solvated in water; the second, containing the rest of the molecule, lay down on the water surface. In contrast to these results, the molecule at the water−CCl4 interface was straight on average, with a inclination of approximately 40° from the surface normal.

Spinodal of liquid water

Abstract: An open question in the study of water concerns the shape of the liquid spinodal line in the phase diagram of water, a boundary which represents the limit of mechanical stability of the liquid state. It has been conjectured that the pressure of the liquid spinodal ${\mathit{P}}_{\mathit{s}}$(T) does not decrease monotonically with decreasing temperature T, but passes through a minimum and is ``reentrant'' from negative to positive pressure P in a region of T in which the liquid is deeply supercooled. The conjectured minimum in ${\mathit{P}}_{\mathit{s}}$(T) has not been directly observed due to the difficulties encountered in experiments which attempt to study liquid water under tension. Here we exploit the ability of molecular-dynamics computer simulations to model the behavior of liquid water deep into its metastable region. We thereby attempt to observe a minimum in ${\mathit{P}}_{\mathit{s}}$(T). We first argue that the ST2 potential of Stillinger and Rahman [J. Chem. Phys. 60, 1545 (1974)] is the best of several commonly used water interaction potentials for this purpose. Then, we conduct simulations of a system of ST2 particles over a wide range of stable and metastable liquid-state points, and demonstrate that ${\mathit{P}}_{\mathit{s}}$(T) for ST2 is not reentrant. In a second set of simulations we test if the behavior we find is limited to the ST2 potential by exploring the relevant thermodynamic region of the liquid as simulated by the TIP4P interaction potential of Jorgensen et al. [J. Chem. Phys. 79, 926 (1983)]. We find that the TIP4P potential confirms the absence of a reentrant spinodal. We also show how the structural and energetic properties of both the ST2 and TIP4P liquids are consistent with the absence of a reentrant spinodal.

A smooth particle mesh Ewald method

Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

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.

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

Quantum mechanical continuum solvation models.

Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072