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Papers by Sherwin Singer

The Journal of Physical Chemistry B, 2015

We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system... more We investigate the DNA-silica binding mechanism using molecular dynamics simulations. This system is of technological importance, and also of interest to explore how negatively charged DNA can bind to a silica surface, which is also negatively charged at pH values above its isoelectric point near pH 3. We find that the two major binding mechanisms are attractive interactions between DNA phosphate and surface silanol groups and hydrophobic bonding between DNA base and silica hydrophobic region. Umbrella sampling and the weighted histogram analysis method (WHAM) are used to calculate the free energy surface for detachment of DNA from a binding configuration to a location far from the silica surface. Several factors explain why single-stranded DNA (ssDNA) has been observed to be more strongly attracted to silica than double-stranded (dsDNA): (1) ssDNA is more flexible and therefore able to maximize the number of binding interactions. (2) ssDNA has free unpaired bases to form hydrophobic attachment to silica while dsDNA has to break hydrogen bonds with base partners to get free bases. (3) The linear charge density of dsDNA is twice that of ssDNA. We devise a procedure to approximate the atomic forces between biomolecules and amorphous silica to enable large-scale biomolecule-silica simulations as reported here.

Physical review. E, Statistical, nonlinear, and soft matter physics, 2003

Ice-Ih consists of a disordered hydrogen-bonded network. The degree of disorder in ice-Ih, and po... more Ice-Ih consists of a disordered hydrogen-bonded network. The degree of disorder in ice-Ih, and possible phase transitions to an ordered phase have been debated in recent years. The dependence of energy, free energy, and other scalar physical properties on H-bond topology is needed to understand these phenomena. Graph invariants provide a means of linking physical properties to the topology of the H-bond network. We have previously shown the effectiveness of graph invariants for finite water clusters [J.-L. Kuo, J. V. Coe, S. J. Singer, Y. B. Band, and L. Ojamäe, J. Chem. Phys., 114, 2527 (2001)]. In this work, we develop a formalism for the graph invariants of periodic systems. We demonstrate that graph invariants for small unit cells are a subset of the graph invariants of larger unit cells, providing a hierarchy of approximations by which detailed calculations for small unit cells, such as periodic ab initio calculations as they become available, can be used to parametrize the ene...

Physical Review E, 2001

We derive an analytic scaling theory for a two-dimensional system in which spontaneous patterns o... more We derive an analytic scaling theory for a two-dimensional system in which spontaneous patterns of stripes, bubbles, and intermediately shaped domains arise due to the competition of short-range attractions and long-range dipolar repulsions. The theory predicts temperature and domain-size scaling as a function of the relative repulsion strength eta, the ratio of the repulsive to the attractive coupling constant in the system's Hamiltonian. As eta decreases, the domain size explodes exponentially and the melting temperature for a system of ordered stripes increases. Our findings shed new light on the phase diagram and critical excitations for the dipolar Ising ferromagnet or lattice gas and their continuum analogs. We show that the features described by the scaling theory are insensitive to details like cutoffs for the dipolar interactions and, therefore, should be widely applicable. Our corresponding states analysis explains the experimentally observed stripe melting upon compression in a Langmuir monolayer. A phenomenological extension of the analytic scaling theory describes how the system's behavior is modified in the presence of magnetization or density fluctuations. Fluctuations are found to suppress domain size and the stripe melting temperature. In regimes where fluctuations are important, we predict that domain size will decrease with increasing temperature.

ABSTRACT Surface freezing, at temperatures up to a few degrees above the equilibrium melting poin... more ABSTRACT Surface freezing, at temperatures up to a few degrees above the equilibrium melting point, has been observed for intermediate chain length (16<= i<= 50) n-alkanes [B. M. Ocko, X. Z. Wu, E. B. Sirota, S. K. Sinha, O. Gang and M. Deutsch, Phys. Rev. E, 1997, 55, 3164-3182]. Our recent experimental results suggest that surface freezing is also the first step when highly supercooled nanodroplets of n-octane crystallize. Our data yield surface and bulk nucleation rates on the order of ~1015/cm2.s and ~1022/cm3.s, respectively. Complementary molecular dynamics simulations also show that the surface of the droplet freezes almost immediately, and freezing of the remainder of the droplet progresses in a layer-by-layer manner.

Physical Review Letters, 2000

A model with competing short-ranged attractions and long-ranged repulsions that describes self-or... more A model with competing short-ranged attractions and long-ranged repulsions that describes self-organized patterns in systems like Langmuir monolayers, magnetic films, and adsorbed monolayers is studied using numerical simulations and analytic theory. Simulations provide strong evidence confirming that the stripe phase order is destroyed in a defect unbinding transition. Large scale computer simulations are in agreement with an analytic scaling theory, which also predicts an eventual crossover from defect-mediated stripe melting to a spin-disordering (or particle-mixing) mechanism with decreasing repulsion strength.

Physical Review E, 2005

Electro-osmotic flow is studied by nonequilibrium molecular dynamics simulations in a model syste... more Electro-osmotic flow is studied by nonequilibrium molecular dynamics simulations in a model system chosen to elucidate various factors affecting the velocity profile and facilitate comparison with existing continuum theories. The model system consists of spherical ions and solvent, with stationary, uniformly charged walls that make a channel with a height of 20 particle diameters. We find that hydrodynamic theory adequately describes simple pressure-driven (Poiseuille) flow in this model. However, Poisson-Boltzmann theory fails to describe the ion distribution in important situations, and therefore continuum fluid dynamics based on the Poisson-Boltzmann ion distribution disagrees with simulation results in those situations. The failure of Poisson-Boltzmann theory is traced to the exclusion of ions near the channel walls resulting from reduced solvation of the ions in that region. When a corrected ion distribution is used as input for hydrodynamic theory, agreement with numerical simulations is restored. An analytic theory is presented that demonstrates that repulsion of the ions from the channel walls increases the flow rate, and attraction to the walls has the opposite effect. A recent numerical study of electro-osmotic flow is reanalyzed in the light of our findings, and the results conform well to our conclusions for the model system.

Physical Review E, 2006

Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled und... more Ice Ih, ordinary ice at atmospheric pressure, is a proton-disordered crystal that when cooled under special conditions is believed to transform to ferroelectric proton-ordered ice XI, but this transformation is still subject to controversy. Ice VII, also proton disordered throughout its region of stability, transforms to proton-ordered ice VIII upon cooling. In contrast to the ice Ih/XI transition, the VII/VIII transition and the crystal structure of ice VIII are well characterized. In order to shed some light on the ice Ih proton ordering transition, we present the results of periodic electronic density functional theory calculations and statistical simulations. We are able to describe the small energy differences among the innumerable H-bond configurations possible in a large simulation cell by using an analytic theory to extrapolate from electronic DFT calculations on small unit cells to cells large enough to approximate the thermodynamic limit. We first validate our methods by comparing our predictions to the well-characterized ice VII/VIII proton ordering transition, finding agreement with respect to both the transition temperature and structure of the low-temperature phase. For ice Ih, our results indicate that a proton-ordered phase is attainable at low temperatures, the structure of which is in agreement with the experimentally proposed ferroelectric Cmc2 1 structure. The predicted transition temperature of 98 K is in qualitative agreement with the observed transition at 72 K on KOH-doped ice samples.

Journal of the American Chemical Society, 2007

We report experimental and theoretical studies on water and protein dynamics following photoexcit... more We report experimental and theoretical studies on water and protein dynamics following photoexcitation of apomyoglobin. Using site-directed mutation and with femtosecond resolution, we experimentally observed relaxation dynamics with a biphasic distribution of time scales, 5 and 87 ps, around the site Trp7. Theoretical studies using both linear response and direct nonequilibrium molecular dynamics (MD) calculations reproduced the biphasic behavior. Further constrained MD simulations with either frozen protein or frozen water revealed the molecular mechanism of slow hydration processes and elucidated the role of protein fluctuations. Observation of slow water dynamics in MD simulations requires protein flexibility, regardless of whether the slow Stokes shift component results from the water or protein contribution. The initial dynamics in a few picoseconds represents fast local motions such as reorientations and translations of hydrating water molecules, followed by slow relaxation involving strongly coupled water-protein motions. We observed a transition from one isomeric protein configuration to another after 10 ns during our 30 ns ground-state simulation. For one isomer, the surface hydration energy dominates the slow component of the total relaxation energy. For the other isomer, the slow component is dominated by protein interactions with the chromophore. In both cases, coupled water-protein motion is shown to be necessary for observation of the slow dynamics. Such biologically important water-protein motions occur on tens of picoseconds. One significant discrepancy exists between theory and experiment, the large inertial relaxation predicted by simulations but clearly absent in experiment. Further improvements required in the theoretical model are discussed.

Chemical Physics Letters, 1983

Abstract Electronic relaxation processes in solution in which intramolecular potential barriers t... more Abstract Electronic relaxation processes in solution in which intramolecular potential barriers to reactive motion are absent are modelled by brownian motion of a solute particle on a harmonic surface with a position-dependent sink. The resulting FokkerPlanck equation ...

Biophysical Journal, 2009

ABSTRACT Exposure to far UV radiation induces DNA damage in the form of cyclobutane pyrimidine di... more ABSTRACT Exposure to far UV radiation induces DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Cyclobutane dimer lesions can be repaired by the enzyme photolyase, in which the absorption of a blue light photon initiates a sequence of photochemical events leading to the injection of an electron at the site of the CPD lesion in DNA. The electron catalyzes the repair of the cyclobutane dimer, splitting the CPD to is original pyrimidine units, and is subsequently recaptured by the photolyase protein. In this work we investigate the molecular mechanism of the repair of the cyclobutane dimer radical anion in aqueous solution using ab initio MD simulations. Umbrella sampling is used to determine a two-dimensional free energy surface as a function of the C5-C5-4 and C6-C6-4 distances. The neutral dimer is unable to surmount a large free energy barrier for repair. Upon addition of an electron, the splitting of the C5-C5-4 coordinate is virtually barrier less. Transition state theory predicts that the splitting of the C6-C6-4 bond is complete on a picosecond timescale. The free energy surface suggests that the splitting of the two bonds is asynchronously concerted. Our work is the first to explicitly include the electronic degrees of freedom for both the cyclobutane dimer and the surrounding water pocket. The ab initio simulations show that at least 30% of the electron density is delocalized onto the surrounding solvent during the splitting process. Simulations on the neutral surface show that back electron transfer from the dimer is critical for the completion of splitting: splitting of the C5-C5' and C6-C6' bonds can be reversed or enhanced depending on when electron return occurs. To maximize splitting yield, the back electron transfer should occur beyond the transition state along the splitting coordinate. Non-equilibrium trajectories are also conducted that begin with the electron added to a neutral unrepaired solvated CPD. Our results indicate that there are two sup-populations: the first population with the C5-C5' bond splitting spontaneously, as indicated by our two-dimensional free energy surface, and a second population where the C5-C5' bond remains intact over the first half of a picosecond.